A novel application of data-consistent inversion to overcome spurious inference in genome-wide association studies.

The genome-wide association studies (GWAS) typically use linear or logistic regression models to identify associations between phenotypes (traits) and genotypes (genetic variants) of interest. However, the use of regression with the additive assumption has potential limitations. First, the normality assumption of residuals is the one that is rarely seen in practice, and deviation from normality increases the Type-I error rate. Second, building a model based on such an assumption ignores genetic structures, like, dominant, recessive, and protective-risk cases. Ignoring genetic variants may result in spurious conclusions about the associations between a variant and a trait. We propose an assumption-free model built upon data-consistent inversion (DCI), which is a recently developed measure-theoretic framework utilized for uncertainty quantification. This proposed DCI-derived model builds a nonparametric distribution on model inputs that propagates to the distribution of observed data without the required normality assumption of residuals in the regression model. This characteristic enables the proposed DCI-derived model to cover all genetic variants without emphasizing on additivity of the classic-GWAS model. Simulations and a replication GWAS with data from the COPDGene demonstrate the ability of this model to control the Type-I error rate at least as well as the classic-GWAS (additive linear model) approach while having similar or greater power to discover variants in different genetic modes of transmission.

In Situ Polymerization Bi-Functional Gel Polymer Electrolyte for High Performance Quasi-Solid-State Lithium-Sulfur Batteries.

Lithium-sulfur (Li-S) batteries are expected to be the next-generation energy storage system due to the ultrahigh theoretical energy density and low cost. However, the notorious shuttle effect of higher-order polysulfides and the uncontrollable lithium dendrite growth are the two biggest challenges for commercially viable Li-S batteries. Herein, these two main challenges are solved by in situ polymerization of bi-functional gel polymer electrolyte (GPE). The initiator (SiCl4) not only drives the polymerization of 1,3-dioxolane (DOL) but also induces the construction of a hybrid solid electrolyte interphase (SEI) with inorganic-rich compositions on the Li anode. In addition, diatomaceous earth (DE) is added and anchored in the GPE to obtain PDOL-SiCl4-DE electrolyte through in situ polymerization. Combined with density functional theory (DFT) calculations, the hybrid SEI provides abundant adsorption sites for the deposition of Li+, inhibiting the growth of lithium dendrites. Meanwhile, the shuttle effect is greatly alleviated due to the strong adsorption capacity of DE toward lithium polysulfides. Therefore, the Li/Li symmetric cell and Li-S full cell assembled with PDOL-SiCl4-DE exhibit excellent cycling stability. This study offers a valuable reference for the development of high performance and safe Li-S batteries.

An Intrinsic Stable Layered Oxide Cathode for Practical Sodium-Ion Battery: Solid Solution Reaction, Near-Zero-Strain and Marvelous Water Stability.

Non-aqueous solvents, in particular N,N-dimethylaniline (NMP), are widely applied for electrode fabrication since most sodium layered oxide cathode materials are readily damaged by water molecules. However, the expensive price and poisonousness of NMP unquestionably increase the cost of preparation and post-processing. Therefore, developing an intrinsically stable cathode material that can implement the water-soluble binder to fabricate an electrode is urgent. Herein, a stable nanosheet-like Mn-based cathode material is synthesized as a prototype to verify its practical applicability in sodium-ion batteries (SIBs). The as-prepared material displays excellent electrochemical performance and remarkable water stability, and it still maintains a satisfactory performance of 79.6% capacity retention after 500 cycles even after water treatment. The in situ X-ray diffraction (XRD) demonstrates that the synthesized material shows an absolute solid-solution reaction mechanism and near-zero-strain. Moreover, the electrochemical performance of the electrode fabricated with a water-soluble binder shows excellent long-cycling stability (67.9% capacity retention after 500 cycles). This work may offer new insights into the rational design of marvelous water stability cathode materials for practical SIBs.

Defective Diamane: A Superior Sensor for Toxic Gases Capture and Detection with Excellent Selectivity, Sensitivity, and Reversibility at Room Temperature.

The toxic gases emitted from industrial production have caused significant damage to the environment and human health, necessitating efficient gas sensors for their detection and removal. In this work, first-principles calculations are employed to investigate the potential application of diamanes for high-performance toxic gas sensors. The results show that nine gas molecules (CO, CO2, NO, NO2, NH3, SO2, N2, O2, and H2O) are physisorbed on pristine diamane by weak van der Waals interactions. After introducing H/F defects, diamane can effectively capture specific toxic gases (CO, NO, NO2, and SO2) in the presence of interfering gases (N2, O2, and H2O), suggesting excellent selectivity and anti-interference ability. Orbital hybridization and significant charge redistribution between gas molecules and defective diamane dominate the enhanced adsorbate-substrate interactions. More importantly, the high sensitivity and good reversibility of defective diamane for detecting CO, NO, and SO2 molecules enable its reuse as a superior resistance-type gas sensor. Our calculations provide valuable insights into the potential of defective diamane for detecting toxic gases and shed light on the practical application of novel carbon-based materials in the gas-sensing field.

Bacillus licheniformis Jrh14-10 enhances alkaline tolerance in Arabidopsis thaliana by regulating crosstalk between ethylene and polyamine pathways.

Plant growth-promoting rhizobacteria (PGPR) are known for their role in ameliorating plant stress, including alkaline stress, yet the mechanisms involved are not fully understood. This study investigates the impact of various inoculum doses of Bacillus licheniformis Jrh14-10 on Arabidopsis growth under alkaline stress and explores the underlying mechanisms of tolerance enhancement. We found that all tested doses improved the growth of NaHCO3-treated seedlings, with 109 cfu/mL being the most effective. Transcriptome analysis indicated downregulation of ethylene-related genes and an upregulation of polyamine biosynthesis genes following Jrh14-10 treatment under alkaline conditions. Further qRT-PCR analysis confirmed the suppression of ethylene biosynthesis and signaling genes, alongside the activation of polyamine biosynthesis genes in NaHCO3-stressed seedlings treated with Jrh14-10. Genetic analysis showed that ethylene signaling-deficient mutants (etr1-3 and ein3-1) exhibited greater tolerance to NaHCO3 than the wild type, and the growth-promoting effect of Jrh14-10 was significantly diminished in these mutants. Additionally, Jrh14-10 was found unable to produce 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indicating it does not reduce the ethylene precursor ACC in Arabidopsis. However, Jrh14-10 treatment increased the levels of polyamines (putrescine, spermidine, and spermine) in stressed seedlings, with spermidine particularly effective in reducing H2O2 levels and enhancing Fv/Fm under NaHCO3 stress. These findings reveal a novel mechanism of PGPR-induced alkaline tolerance, highlighting the crosstalk between ethylene and polyamine pathways, and suggest a strategic redirection of S-adenosylmethionine towards polyamine biosynthesis to combat alkaline stress.

Clinical characteristics of viral-associated Fuchs uveitis syndrome and Posner-Schlossman syndrome in a Chinese population.

PURPOSE: To identify the types of viral infection in aqueous humor (AqH) among patients diagnosed as Fuchs uveitis syndrome (FUS) or Posner-Schlossman syndrome (PSS) and investigate their relevance to clinical manifestations and visual outcome. METHODS: A total of 375 patients and 171 patients were diagnosed as FUS or PSS in our department. AqH and serum samples from 68 FUS patients and 16 PSS patients were obtained during eye surgery. The viral etiologies, clinical features, auxiliary tests and visual prognosis of patients with FUS or PSS who underwent AqH analysis were analysed and compared. RESULTS: Among 68 FUS patients, rubella virus (RV), cytomegalovirus (CMV), herpes simplex virus (HSV) and varicella-zoster virus were identified in 17, 11, 1 and 1 patients, respectively. Seven patients with CMV and 1 with HSV were identified in 16 PSS patients. In both FUS and PSS groups, virus-associated eyes had higher proportion of secondary glaucoma and worse visual prognosis as compared with non-virus-associated eyes (all P < 0.05). In FUS group, specifically, CMV infection manifested as more obvious anterior segment inflammation and lower corneal endothelial cell density (CECD). RV infection showed a higher percentage of vitritis. In PSS group, CMV-associated PSS had a lower retinal nerve fiber layer thickness and CECD, worse visual prognosis as compared with non-virus-associated PSS (all P < 0.05). CONCLUSION: Our study identified 4 types of viral infection in FUS and 2 types of viral infection in PSS. Virus-associated patients are usually associated with more obvious clinical signs and poor visual prognosis.

Surface Lattice Modulation through Chemical Delithiation toward a Stable Nickel-Rich Layered Oxide Cathode.

Nickel-rich layered oxides (NLOs) are considered as one of the most promising cathode materials for next-generation high-energy lithium-ion batteries (LIBs), yet their practical applications are currently challenged by the unsatisfactory cyclability and reliability owing to their inherent interfacial and structural instability. Herein, we demonstrate an approach to reverse the unstable nature of NLOs through surface solid reaction, by which the reconstructed surface lattice turns stable and robust against both side reactions and chemophysical breakdown, resulting in improved cycling performance. Specifically, conformal La(OH)3 nanoshells are built with their thicknesses controlled at nanometer accuracy, which act as a Li+ capturer and induce controlled reaction with the NLO surface lattices, thereby transforming the particle crust into an epitaxial layer with localized Ni/Li disordering, where lithium deficiency and nickel stabilization are both achieved by transforming oxidative Ni3+ into stable Ni2+. An optimized balance between surface stabilization and charge transfer is demonstrated by a representative NLO material, namely, LiNi0.83Co0.07Mn0.1O2, whose surface engineering leads to a highly improved capacity retention and excellent rate capability with a strong capability to inhibit the crack of NLO particles. Our study highlights the importance of surface chemistry in determining chemical and structural behaviors and paves a research avenue in controlling the surface lattice for the stabilization of NLOs toward reliable high-energy LIBs.

TET2-mediated upregulation of 5-hydroxymethylcytosine in LRRC39 promoter promotes Th1 response in association with downregulated Treg response in Vogt-Koyanagi-Harada disease.

DNA 5-Hydroxymethylcytosine (5-hmC), an oxidative reaction mediated by the ten-eleven translocation (TET) family, has been reported to play an essential role in the progression of auto-inflammatory and autoimmune diseases. By far, little is known about the effect of DNA 5-hmC and the TET family on the development of Vogt-Koyanagi-Harada (VKH) disease. In this study, we discovered that the global DNA 5-hmC level and the TET activity were elevated in association with the up-regulated expression of TET2 at both mRNA and protein levels in CD4+T cells from active VKH patients compared to healthy controls. Integrated analysis of DNA 5-hmC pattern and transcription profile of CD4+ T cells revealed that 6 candidate target genes were involved in the development of VKH disease. The promoter 5-hmC and mRNA levels of leucine rich repeat containing 39 (LRRC39) were verified to be elevated in active VKH patients. Functional experiments showed that TET2 could up-regulate LRRC39 mRNA expression by increasing the promoter 5-hmC level of LRRC39 in CD4+ T cells from active VKH patients. Up-regulated LRRC39 expression could increase the frequencies of IFN-γ+ and IL-17+ CD4+ T cells as well as the secretions of IFN-γ and IL-17 in association with the decreased frequency of CD4+CD25+FOXP3+ regulatory T (Treg) cells and the reduced production of IL-10. Additionally, restoration of LRRC39 rescued TET2-silencing-mediated reduced frequency of IFN-γ+ CD4+ T cells and increased frequency of CD4+CD25+FOXP3+ Treg cells. Collectively, our study reveals a novel axis, the TET2-5-hmC-LRRC39-Th1/Treg responses axis, in the pathogenesis of VKH and provides a potential target for further investigation into the epigenetic therapy of this disease.

High-Performance Solid Lithium Metal Batteries Enabled by LiF/LiCl/LiIn Hybrid SEI via InCl3 -Driven In Situ Polymerization of 1,3-Dioxolane.

The use of poly(1,3-dioxolane) (PDOL) electrolyte for lithium batteries has gained attention due to its high ionic conductivity, low cost, and potential for large-scale applications. However, its compatibility with Li metal needs improvement to build a stable solid electrolyte interface (SEI) toward metallic Li anode for practical lithium batteries. To address this concern, this study utilized a simple InCl3 -driven strategy for polymerizing DOL and building a stable LiF/LiCl/LiIn hybrid SEI, confirmed through X-ray photoelectron spectroscopy (XPS) and cryogenic-transmission electron microscopy (Cryo-TEM). Furthermore, density functional theory (DFT) calculations and finite element simulation (FES) verify that the hybrid SEI exhibits not only excellent electron insulating properties but also fast transport properties of Li+ . Moreover, the interfacial electric field shows an even potential distribution and larger Li+ flux, resulting in uniform dendrite-free Li deposition. The use of the LiF/LiCl/LiIn hybrid SEI in Li/Li symmetric batteries shows steady cycling for 2000 h, without experiencing a short circuit. The hybrid SEI also provided excellent rate performance and outstanding cycling stability in LiFePO4 /Li batteries, with a high specific capacity of 123.5 mAh g-1 at 10 C rate. This study contributes to the design of high-performance solid lithium metal batteries utilizing PDOL electrolytes.

Structural stability and electronic and mechanical properties of nitrogen- and boron-doped fluorinated diamane.

In this work, the structural, electronic and mechanical properties of fluorinated diamane (F-diamane) with N and B dopants are systemically investigated using first-principles calculation. The N atom tends to stay in the external substituted site without F saturation, while the B-doped structure of the substituted external site with F saturation is the most stable. Ab initio molecular dynamics simulations confirm the thermal stability. The band structures of stable doped structures are similar to that of pristine F-diamane, due to the slight contribution of the dopant to the band edges. In addition, after the introduction of the B dopant, the formation energy reduces, and the transition barrier of graphene bilayers into diamane is smaller, indicating the feasibility of graphene bilayer fluoridation. Furthermore, we find that these doped structures have mechanical stability with isotropic elastic constants, Young's modulus, shear modulus and Poisson's ratio. Our work would promote the synthesis and development of two-dimensional diamane.

Emerging Relevance of Ghrelin in Programmed Cell Death and Its Application in Diseases.

Ghrelin, comprising 28 amino acids, was initially discovered as a hormone that promotes growth hormones. The original focus was on the effects of ghrelin on controlling hunger and satiation. As the research further develops, the research scope of ghrelin has expanded to a wide range of systems and diseases. Nevertheless, the specific mechanisms remain incompletely understood. In recent years, substantial studies have demonstrated that ghrelin has anti-inflammatory, antioxidant, antiapoptotic, and other effects, which could affect the signaling pathways of various kinds of programmed cell death (PCD) in treating diseases. However, the regulatory mechanisms underlying the function of ghrelin in different kinds of PCD have not been thoroughly illuminated. This review describes the relationship between ghrelin and four kinds of PCD (apoptosis, necroptosis, autophagy, and pyroptosis) and then introduces the clinical applications based on the different features of ghrelin.

Genome-Wide Identification and Analysis Uncovers the Potential Role of JAZ and MYC Families in Potato under Abiotic Stress.

As key regulators of the Jasmonates (JAs) signal transduction pathway, JAZ protein, and MYC transcription factors are imperative for plant response to external environmental changes, growth, and development. In this study, 18 StJAZs and 12 StMYCs were identified in potatoes. Their chromosomal position, phylogenetic development, gene structure, and promoter cis-acting parts of the StJAZ genes were analyzed. In addition, Protein-Protein Interaction (PPI) network analysis of StJAZ and StMYC gene families and yeast two-hybrid assay demonstrated that five StMYCs can interact with 16 StJAZs, which provides new insights into the operation mechanism of StJAZs and StMYCs in JA signal response. Moreover, we explored the expression profiles of StJAZs and StMYCs genes in different tissues and during abiotic stresses by RNA-seq data. Based on the PPI network and transcriptome data, the genes StJAZ11, StJAZ16, and StMYC6 were chosen for further qRT-PCR study under salt or mannitol treatment. Under mannitol-induced drought or salinity treatment, the expression patterns of StMYC6, StJAZ11, and StJAZ16 were different, indicating that the JAZ protein and MYC transcription factor may be engaged in the response of potatoes to abiotic stress, which opened up a new research direction for the genetic improvement of potatoes in response to environmental stress.

Plasmonic LAMP: Improving the Detection Specificity and Sensitivity for SARS-CoV-2 by Plasmonic Sensing of Isothermally Amplified Nucleic Acids.

The ability to detect pathogens specifically and sensitively is critical to combat infectious diseases outbreaks and pandemics. Colorimetric assays involving loop-mediated isothermal amplification (LAMP) provide simple readouts yet suffer from the intrinsic non-template amplification. Herein, a highly specific and sensitive assay relying on plasmonic sensing of LAMP amplicons via DNA hybridization, termed as plasmonic LAMP, is developed for the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) RNA detection. This work has two important advances. First, gold and silver (Au-Ag) alloy nanoshells are developed as plasmonic sensors that have 4-times stronger extinction in the visible wavelengths and give a 20-times lower detection limit for oligonucleotides over Au counterparts. Second, the integrated method allows cutting the complex LAMP amplicons into short repeats that are amendable for hybridization with oligonucleotide-functionalized Au-Ag nanoshells. In the SARS-CoV-2 RNA detection, plasmonic LAMP takes ≈75 min assay time, achieves a detection limit of 10 copies per reaction, and eliminates the contamination from non-template amplification. It also shows better detection specificity and sensitivity over commercially available LAMP kits due to the additional sequence identification. This work opens a new route for LAMP amplicon detection and provides a method for virus testing at its early representation.

Comprehensive Analysis of Fragile X Syndrome: Full Characterization of the FMR1 Locus by Long-Read Sequencing.

BACKGROUND: Fragile X syndrome (FXS) is the most frequent cause of inherited X-linked intellectual disability. Conventional FXS genetic testing methods mainly focus on FMR1 CGG expansions and fail to identify AGG interruptions, rare intragenic variants, and large gene deletions. METHODS: A long-range PCR and long-read sequencing-based assay termed comprehensive analysis of FXS (CAFXS) was developed and evaluated in Coriell and clinical samples by comparing to Southern blot analysis and triplet repeat-primed PCR (TP-PCR). RESULTS: CAFXS accurately detected the number of CGG repeats in the range of 93 to at least 940 with mass fraction of 0.5% to 1% in the background of normal alleles, which was 2-4-fold analytically more sensitive than TP-PCR. All categories of mutations detected by control methods, including full mutations in 30 samples, were identified by CAFXS for all 62 clinical samples. CAFXS accurately determined AGG interruptions in all 133 alleles identified, even in mosaic alleles. CAFXS successfully identified 2 rare intragenic variants including the c.879A > C variant in exon 9 and a 697-bp microdeletion flanking upstream of CGG repeats, which disrupted primer annealing in TP-PCR assay. In addition, CAFXS directly determined the breakpoints of a 237.1-kb deletion and a 774.0-kb deletion encompassing the entire FMR1 gene in 2 samples. CONCLUSIONS: Long-read sequencing-based CAFXS represents a comprehensive assay for identifying FMR1 CGG expansions, AGG interruptions, rare intragenic variants, and large gene deletions, which greatly improves the genetic screening and diagnosis for FXS.

Aquaporin 5 Facilitates Corneal Epithelial Wound Healing and Nerve Regeneration by Reactivating Akt Signaling Pathway.

Aquaporins (AQPs) are a highly conserved group of membrane proteins that play critical roles in water and small solute transport across epithelial and endothelial barriers. The aim of this study was to determine whether AQP5, a well-known water channel protein, also plays a role in corneal epithelial wound healing. AQP5 knockout (AQP5-/-) mice were generated using CRISPR/Cas9. A corneal wound healing model was established using epithelial debridement of corneas. The time to corneal epithelial and nerve regeneration was significantly delayed in the AQP5-/- mice. Reduction in Ki-67-positive cells and nerve growth factor (NGF) expression was confirmed in the AQP5-/- mice during healing. Epithelial and nerve regeneration rates were significantly increased in the AQP5-/- mice after treatment with NGF, which was accompanied by recovered levels of phosphorylated Akt. NGF treatment also improved the recovery of corneal nerve fiber density and sensitivity in the AQP5-/- mice. While the promotion of NGF induced corneal epithelial and nerve regeneration, Akt inhibitor reversed Akt reactivation. A significant impairment of corneal wound healing in the AQP5-/- mice resulted from distinct defects in corneal epithelial cell proliferation and nerve regeneration. These results provide evidence for the involvement of aquaporin in cell proliferation and suggest that AQP5 induction could be a potential therapy for accelerating the resurfacing of corneal defects.

Association of macular corneal dystrophy with excessive cell senescence and apoptosis induced by the novel mutant CHST6.

Macular corneal dystrophy (MCD) is a rare form of hereditary corneal dystrophy caused by CHST6 mutations. Owing to the genetic heterogeneity and population differences among patients with MCD, the genetic cause of MCD has not been fully elucidated, and the pathogenesis underlying the genetic mutation is still unclear. In this study, Chinese families and sporadic patients were included as subjects, and clinical and genetic analyses were performed to detect novel CHST6 mutations. In addition, the underlying pathogenic mechanisms of MCD were investigated by in vitro cell experiments. Two consanguineously married families and 10 sporadic patients with MCD were enrolled. Direct sequencing of the CHST6 gene was performed in all the patients to identify novel mutations. Wild-type and mutant overexpression cell lines were constructed to study the effects of the mutation in vitro. The expressions of endoplasmic reticulum (ER) stress markers and apoptotic factors, cell senescence, and migration levels tests were performed in different overexpression cell lines. As a result, four novel mutations (R155Afs*66, S84Cfs*17, E71G, and E71Q) and 10 previously reported mutations in the CHST6 gene were identified. Among the reported mutations, the most frequent mutations detected in the patients were L21Rfs*88 (4/14) and L21H (4/14). All the novel mutations were absent in the 50 healthy controls and were predicted to alter highly conserved amino acids across the different species and considered to be "disease causing" by function prediction. The results of the in vitro cell experiment further demonstrated that the novel homozygous frameshift mutations (S84Cfs*17 and R155Afs*66) of CHST6 detected in the consanguineously married families could lead to truncated proteins with defect functions, higher ER stress and apoptotic levels, decreased cell migration, and excessive cell senescence in corneal stromal cells, thereby affecting the normal functions of corneal stromal cells. These changes might play important roles in corneal opacity, which is characteristic of corneas with MCD. Our study extended the existing spectrum of disease-causing mutations and further elucidated the underlying pathogenic mechanisms of MCD.

Structural and electronic properties of pristine and hydrogen-terminated c-BN(100) surfaces.

Semiconductor surfaces are crucially important for electronics, but it is difficult to directly image their surface structures. In this work, the surface structures and electronic properties of pristine and H-terminated c-BN(100) surfaces are predicted by first principles calculation. It is found that the surfaces with reconstructed dimers and staggered dimers are thermally and dynamically stable. When the surface N and B atoms are saturated with the virtual H of 0.5 e and 1.5 e, the surface states near Fermi level are nearly removed, and have the wide bandgaps. Meanwhile, after surface hydrogenation, the electron affinity value changes from positive to negative. Our findings could provide a theoretical guidance for designing c-BN-based electronic devices.

Lacrimal gland homeostasis is maintained by the AQP5 pathway by attenuating endoplasmic reticulum stress inflammation in the lacrimal gland of AQP5 knockout mice.

Purpose: AQP5-/- mice spontaneously exhibit dry eye symptoms. The purpose of this study was to assess the endoplasmic reticulum (ER) stress-mediated inflammation generated by a deficiency of aquaporin 5 (AQP5) in the lacrimal gland. Methods: Hematoxylin and eosin (H&E) staining, Oil Red O staining, and transmission electron microscopy (TEM) analysis were performed to identify structural changes in lacrimal gland epithelial cells because of AQP5 deficiency. Corneal epithelial defects were assessed with sodium fluorescein staining. The expression profiles of mRNA and proteins were determined by quantitative real-time reverse transcription PCR (qRT-PCR) and western blot. Mice in the quercetin group were injected intraperitoneally with 40 mg/kg of quercetin, and the control group was injected with an equal volume of dimethyl sulfoxide (DMSO) for 4 weeks. Results: Aqueous tear secretion fell at about 50% in 1- and 6-month-old AQP5-/- mice compared with that of AQP5+/+ mice. TEM showed that the ER structure was damaged. ER stress was significantly increased in the lacrimal gland of AQP5-/- mice. Lipid droplets accumulated in the matrix and acinar cells, and changes occurred in the lipid metabolism and gene expression levels for PPARα, CPT1α, and CPT2 in the AQP5-/- mice. Immune cell infiltration and increases in the gene expression levels of the chemokines CXCL1, CXCL2, and CCL5 were found in the lacrimal gland of AQP5-/- mice. Quercetin partially reversed ER stress levels, inflammation, and lipid accumulation, and it inhibited tear secretion. Conclusions: The study data indicated that a deficiency of AQP5 induced pathophysiological changes and functional decompensation of the lacrimal gland. Quercetin may improve the inflammation in the lacrimal glands of AQP5-/- mice by regulating the ER stress levels.

AQP5 regulates vimentin expression via miR-124-3p.1 to protect lens transparency.

The pathogenesis of congenital cataract (CC), a major disease associated with blindness in infants, is complex and diverse. Aquaporin 5 (AQP5) represents an essential membrane water channel. In the present study, whole exome sequencing revealed a novel heterozygous missense mutation of AQP5 (c.152 T > C, p. L51P) in the four generations of the autosomal dominant CC (adCC) family. By constructing a mouse model of AQP5 knockout (KO) using the CRISPR/Cas9 technology, we observed that the lens of AQP5-KO mice showed mild opacity at approximately six months of age. miR-124-3p.1 expression was identified to be downregulated in the lens of AQP5-KO mice as evidenced by qRT-PCR analysis. A dual luciferase reporter assay confirmed that vimentin was a target gene of miR-124-3p.1. Organ-cultured AQP5-KO mouse lenses were showed increased opacity compared to those of WT mice, and vimentin expression was upregulated as determined by RT-PCR, western blotting, and immunofluorescence staining. After miR-124-3p.1 agomir was added, the lens opacity in WT mice and AQP5-KO mice decreased, accompanied by the downregulation of vimentin. AQP5-L51P increased vimentin expression of in human lens epithelial cells. Therefore, a missense mutation in AQP5 (c.152 T > C, p. L51P) was associated with adCC, and AQP5 could participate in the maintenance of lens transparency by regulating vimentin expression via miR-124-3p.1.

Prediction of protein crotonylation sites through LightGBM classifier based on SMOTE and elastic net.

Lysine crotonylation is an important protein post-translational modification, which plays an important role in the process of chromosome organization and nucleic acid metabolism. Recognition of crotonylation sites is important to understand the function and mechanism of proteins. Traditional experimental methods are time-consuming and expensive, and can't predict crotonylation sites quickly and accurately. Therefore, this paper proposes a novel crotonylation sites prediction method called LightGBM-CroSite. First, binary encoding (BE), position weight amino acid composition (PWAA), encoding based on grouped weight (EBGW), k nearest neighbors (KNN), pseudo-position specific scoring matrix (PsePSSM) are used to extract features of protein sequences and obtain the original feature space. Second, the elastic net is used to remove redundant information and select the optimal feature subset. Third, the synthetic minority oversampling technique (SMOTE) is used to balance the samples. Finally, the balanced feature vectors are input into LightGBM to predict the crotonylation sites. According to the result of jackknife test, the Accuracy (ACC), Matthew's correlation coefficient (MCC) and area under ROC curve (AUC) are 98.99%, 0.9798 and 0.9996, respectively. Compared with other state-of-the-art methods, the results show that our method has a better model performance on the crotonylation sites prediction. The source code and all datasets are available at https://github.com/QUST-AIBBDRC/LightGBM-CroSite/.