Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases.

It's challenging work to identify disease-causing genes from the next-generation sequencing (NGS) data of patients with Mendelian disorders. To improve this situation, researchers have developed many phenotype-driven gene prioritization methods using a patient's genotype and phenotype information, or phenotype information only as input to rank the candidate's pathogenic genes. Evaluations of these ranking methods provide practitioners with convenience for choosing an appropriate tool for their workflows, but retrospective benchmarks are underpowered to provide statistically significant results in their attempt to differentiate. In this research, the performance of ten recognized causal-gene prioritization methods was benchmarked using 305 cases from the Deciphering Developmental Disorders (DDD) project and 209 in-house cases via a relatively unbiased methodology. The evaluation results show that methods using Human Phenotype Ontology (HPO) terms and Variant Call Format (VCF) files as input achieved better overall performance than those using phenotypic data alone. Besides, LIRICAL and AMELIE, two of the best methods in our benchmark experiments, complement each other in cases with the causal genes ranked highly, suggesting a possible integrative approach to further enhance the diagnostic efficiency. Our benchmarking provides valuable reference information to the computer-assisted rapid diagnosis in Mendelian diseases and sheds some light on the potential direction of future improvement on disease-causing gene prioritization methods.

Fabrication of lidocaine-loaded polymer dissolving microneedles for rapid and prolonged local anesthesia.

There is an urgent need for research into effective interventions for pain management to improve patients' life quality. Traditional needle and syringe injection were used to administer the local anesthesia. However, it causes various discomforts, ranging from brief stings to trypanophobia and denial of medical operations. In this study, a dissolving microneedles (MNs) system made of composite matrix materials of polyvinylpyrrolidone (PVP), polyvinyl alcohol (PVA), and sodium hyaluronate (HA) was successfully developed for the loading of lidocaine hydrochloride (LidH). The morphology, size and mechanical properties of the MNs were also investigated. After the insertion of MNs into the skin, the matrix at the tip of the MNs was swelled and dissolved by absorption of interstitial fluid, leading to a rapid release of loaded LidH from MNs' tips. And the LidH in the back patching was diffused into deeper skin tissue through microchannels created by MNs insertion, forming a prolonged anesthesia effect. In addition, the back patching of MNs could be acted as a drug reservoir to form a prolonged local anesthesia effect. The results showed that LidH MNs provided a superior analgesia up to 8 h, exhibiting a rapid and long-lasting analgesic effects. Additionally, tissue sectioning and in vitro cytotoxicity tests indicated that the MNs patch we developed had a favorable biosafety profile.

OsAAP8 mutation leads to significant improvement in the nutritional quality and appearance of rice grains.

Members of the permease gene family are responsible for important biological functions in the growth and development of rice. Here, we show that OsAAP8 is a constitutive expression gene, and its translated protein is localized on the cell membrane. Mutation of the OsAAP8 can promote the expression of genes related to protein and amylopectin synthesis, and also promote the enlargement of protein bodies in its endosperm, leading to an increase in the protein, amylopectin, and total amino acid content of grains in OsAAP8 mutants. Seeds produced by the OsAAP8 mutant were larger, and the chalkiness traits of the OsAAP8 mutants were significantly reduced, thereby improving the nutritional quality and appearance of rice grains. The OsAAP8 protein is involved in the transport of various amino acids; OsAAP8 mutation significantly enhanced the root absorption of a range of amino acids and might affect the distribution of various amino acids. Therefore, OsAAP8 is an important quality trait gene with multiple biological functions, which provides important clues for the molecular design of breeding strategies for developing new high-quality varieties of rice. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01473-w.

Lycorine suppresses the malignancy of breast carcinoma by modulating epithelial mesenchymal transition and ß-catenin signaling.

Lycorine, an isoquinoline alkaloid can exhibit significant anti-cancer effects. The present study was conducted to illustrate the underlying mechanisms of action of lycorine on breast carcinoma under in vitro and in vivo settings Tandem Mass Tag assay and Kyoto Encyclopedia of Genes and Genomes analysis revealed that 20 signaling pathways were closely related to tumorigenesis, especially Wnt signaling pathway and tight junctions. The results demonstrated that lycorine evidently inhibited the proliferation of MDA-MB-231 and MCF-7 cells with IC50 values of 1.84 ± 0.21 µM and 7.76 ± 1.16 µM, respectively. It also blocked cell cycle in G2/M phase, caused a decrease in mitochondrial membrane potential, and induced apoptosis pathways through regulating caspase-3, caspase-8, caspase-9, and PARP expression. Moreover, lycorine effectively repressed the ß-catenin signaling and reversed epithelial-mesenchymal transition (EMT) process. Furthermore, 4T1/Luc homograft tumor model was used to further demonstrate that lycorine significantly inhibited the growth and metastasis of breast tumor. These findings highlight the significance of lycorine as potential anti-neoplastic agent to combat breast cancer.

Berberine inhibits breast carcinoma proliferation and metastasis under hypoxic microenvironment involving gut microbiota and endogenous metabolites.

A potential role of berberine, a benzyl isoquinoline alkaloid, in cancer therapy is apparent. Its underlying mechanisms of berberine against breast carcinoma under hypoxia have not been elucidated. We focused on the doubt how berberine restrains breast carcinoma under hypoxia in vitro and in vivo. A molecular analysis of the microbiome via 16 S rDNA gene sequencing of DNA from mouse faeces confirmed that the abundances and diversity of gut microbiota were significantly altered in 4T1/Luc mice with higher survival rate following berberine treatment. A metabolome analysis liquid chromatography-mass spectrometer/mass spectrometer (LC-MS/MS) revealed that berberine regulated various endogenous metabolites, especially L-palmitoylcarnitine. Furthermore, the cytotoxicity of berberine was investigated in MDA-MB-231, MCF-7, and 4T1 cells. In vitro to simulate under hypoxic environment, MTT assay showed that berberine inhibited the proliferation of MDA-MB-231, MCF-7, and 4T1 cells with IC50 values of 4.14 ± 0.35 µM, 26.53 ± 3.12 µM and 11.62 ± 1.44 µM, respectively. Wound healing and trans-well invasion studies revealed that berberine inhibited the invasion and migration of breast cancer cells. RT-qPCR analysis shed light that berberine reduced the expression of hypoxia-inducible factor-1α (HIF-1α) gene. Immunofluorescence and western blot demonstrated that berberine decreased the expression of E-cadherin and HIF-1α protein. Taken together, these results provide evidence that berberine efficiently suppresses breast carcinoma growth and metastasis in a hypoxic microenvironment, highlighting the potential of berberine as a promising anti-neoplastic agent to combat breast carcinoma.

OsNAC74 affects grain protein content and various biological traits by regulating OsAAP6 expression in rice.

The grain protein content is an important quality trait in cereals, and the expression level of the OsAAP6 can significantly affect the grain protein content in rice. Through site-directed mutagenesis, we found that the position from -7 to -12 bp upstream of the transcription start site of the OsAAP6 was the functional variation site. By using the yeast single hybrid test, point-to-point in yeast, and the local surface plasmon resonance test, the OsNAC74 was screened and verified to be a regulator upstream of OsAAP6. The OsNAC74 is a constitutively expressed gene whose product is located on the cell membrane. The OsAAP6 and the genes related to the seed storage in the Osnac74 mutants were downregulated, and grain protein content was significantly reduced. In addition, OsNAC74 had a significant impact on quality traits such as grain chalkiness and gel consistency in rice. Although the Osnac74 mutant seeds were relatively small, the individual plant yield was not decreased. Therefore, OsNAC74 is an important regulatory factor with multiple biological functions. This study provides important information for the later use of OsNAC74 gene for molecular design and breeding in rice. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01433-w.

Morphological and molecular characterization of a new root-knot nematode, Meloidogyne limonae n. sp. (Nematoda: Meloidogynidae) parasitizing lemon in China.

Root-knot nematodes of the genus Meloidogyne parasitize the roots of thousands of plants and can cause severe damage and yield loss. Here, we report a new root-knot nematode, Meloidogyne limonae n. sp., parasitizing "lemon" (Citrus limon) in Hainan Province, South China. Lemon trees infected by the root-knot nematode showed poor-quality lemons, chlorosis of foliage, weak growth, and numerous root galls with white females and egg masses protruding outside. Phylogenetic trees of sequences within the ribosomal and mitochondria DNA demonstrated that this species differs clearly from other previously described root-knot nematodes. Morphologically, the new species is characterized by an oval-shaped perineal pattern and the lateral field marked by a ridge of cuticle on one or both sides, the dorsal arch is low with fine to coarse, smooth cuticle striae, vulva slit centrally located at the unstriated area; spicules of males are arcuate, curved ventrally; gubernaculum is distinct and curved; labial disc of second-stage juveniles is prominent and dumbbell-shaped; stylet knobs oval and sloping backwardly; pharyngeal glands not filling the body cavity, overlapping intestine ventrally; conical tail gradually tapering. Phylogenetic trees based on ITS1-5.8S-ITS2, D2-D3 of the 28S rDNA, and the COI and COII-16S rRNA genes of the mtDNA showed that Meloidogyne limonae n. sp. belongs to an undescribed root-knot nematode lineage that is separated from other species with the resemblance in morphology, such as M. floridensis M. hispanica, M. acronea, and M. paranaenis.

Occurrence of Root-Knot Nematode (Meloidogyne spp.) on Peppers in Hainan, China, and M. enterolobii and M. incognita Resistance of Common Cultivars.

Root-knot nematodes (Meloidogyne spp.) are the most economically damaging group of plant-parasitic nematodes. They are considered to be a major constraint of pepper (Capsicum annuum L.) crops worldwide. In China, Hainan Island is the main producer of pepper, where the climatic conditions and cropping patterns are favorable for infection by Meloidogyne spp. In this study, we conducted a detailed investigation of the occurrence, severity, and population distribution of root-knot nematodes infesting pepper throughout Hainan Island. We also tested the level of resistance to M. enterolobii and M. incognita of the common pepper cultivars in Hainan. Our results showed that root-knot nematodes belonging to M. enterolobii, M. incognita, and M. javanica were found in Hainan, and the dominant population was M. enterolobii, which is the predominant species in the tropical area. Notably, all the pepper cultivars in this study were highly susceptible to M. enterolobii, which is probably a reason for its rapid spread throughout Hainan. The pepper cultivars exhibited different levels of resistance to M. incognita. This study promotes the comprehensive understanding of the root-knot nematode distribution and host resistance level of Meloidogyne in Hainan, which will guide the effective control of root-knot nematodes.

Recent Advances in Polymer Microneedles for Drug Transdermal Delivery: Design Strategies and Applications.

In recent years, transdermal drug delivery based on microneedles (MNs) technology has received extensive attention, which offers a safer and painless alternative to hypodermic needle injections. They can pierce the stratum corneum and deliver drugs to the epidermis and dermis-structures of skin, showing prominent properties such as minimally invasiveness, bypassing first-pass metabolism, and can be self-administered. A range of materials has been used to fabricate MNs, such as silicon, metal, glass, and polymers. Among them, polymer MNs have gained increasing attention from pharmaceutical and cosmetic companies as one of the promising drug delivery methods. MN products have recently become available on the market, and some of them are under evaluation for efficacy and safety. This paper focuses on the current state of polymer MNs in drug transdermal delivery. The materials and methods for the fabrication of polymer MNs and their drug administration are described. The recent progress of polymer MNs for treatment of cancer, vaccine delivery, blood glucose regulation, androgenetic alopecia, obesity, tissue healing, myocardial infarction, and gout are reviewed. The challenges of MNs technology are summarized and the future development trend of MNs is also prospected.

Neurokinin-1 receptor is an effective target for treating leukemia by inducing oxidative stress through mitochondrial calcium overload.

Substance P (SP) regulates multiple biological processes through its high-affinity neurokinin-1 receptor (NK-1R). While the SP/NK-1R signaling axis is involved in the pathogenesis of solid cancer, the role of this signaling pathway in hematological malignancy remains unknown. Here, we demonstrate that NK-1R expression is markedly elevated in the white blood cells from acute myeloid leukemia patients and a panel of human leukemia cell lines. Blocking NK-1R induces apoptosis in vitro and in vivo via increase of mitochondrial reactive oxygen species. This oxidative stress was triggered by rapid calcium flux from the endoplasmic reticulum into mitochondria and, consequently, impairment of mitochondrial function, a mechanism underlying the cytotoxicity of NK-1R antagonists. Besides anticancer activity, blocking NK-1R produces a potent antinociceptive effect in myeloid leukemia-induced bone pain by alleviating inflammation and inducing apoptosis. These findings thus raise the exciting possibility that the NK-1R antagonists, drugs currently used in the clinic for preventing chemotherapy-induced nausea and vomiting, may provide a therapeutic option for treating human myeloid leukemia.

Development of a Novel Primer-TaqMan Probe Set for Diagnosis and Quantification of Meloidogyne enterolobii in Soil Using qPCR and Droplet Digital PCR Assays.

Early detection of pathogens before the planting season is valuable to forecast disease occurrence. Therefore, rapid and reliable diagnostic approaches are urgently needed, especially for one of the most aggressive root knot nematodes, Meloidogyne enterolobii. In this study, we developed a novel primer-TaqMan probe set aimed at M. enterolobii. The primer-probe set was successfully applied in the identification and quantification of M. enterolobii via qPCR technology. It was also suitable for improved PCR technology, known as ddPCR analyses, and this work presents the first application of this technology for plant parasitic nematodes. Compared with qPCR, ddPCR exhibited better performance with regard to analytical sensitivity, which can provide a more accurate detection of M. enterolobii concealed in field soil. In addition, we generated standard curves to calculate the number of eggs in soil using the qPCR and ddPCR platforms. Hopefully, the results herein will be helpful for forecasting disease severity of M. enterolobii infection and adopting effective management strategies.

Nondestructive determination of soluble solids content and pH in red bayberry (Myrica rubra) based on color space.

Color has strong relationship with food quality. In this paper, partial least square regression (PLSR) and least square-support vector machine (LS-SVM) models combined with six different color spaces (NRGB, CIELAB, CMY, HSI, I1I2I3, and YCbCr) were developed and compared to predict pH value and soluble solids content (SSC) in red bayberry. The results showed that PLSR and LS-SVM models coupled with color space could predict pH value in red bayberry (r = 0.93-0.96, RMSE = 0.09-0.12, MAE = 0.07-0.09, and MRE = 0.04-0.06). In addition, the minimum errors (RMSE = 0.09, MAE = 0.07, and MRE = 0.04) and maximum correlation coefficient value (r = 0.96) were found with the PLSR based on CMY, I1I2I3, and YCbCr color spaces. For predicting SSC, PLSR models based on CIELAB color space (r = 0.90, RMSE = 0.91, MAE = 0.69 and MRE = 0.12) and HSI color space (r = 0.89, RMSE = 0.95, MAE = 0.73 and MRE = 0.13) were recommended. The results indicated that color space combined with chemometric is suitable to non-destructively detect pH value and SSC of red bayberry.

Treatment of Multiple Odontogenic Keratocysts Involving Chinese Patients.

PURPOSE: The optimal treatment of odontogenic keratocysts (OKCs) remains a matter of debate in reported studies. The present study aimed to estimate the postoperative recurrence rates of multiple OKCs (MOKCs) in Chinese patients. MATERIALS AND METHODS: A retrospective cohort study of histologically confirmed MOKCs treated from 2003 to 2017 using enucleation, marsupialization alone, enucleation and peripheral ostectomy, or marsupialization followed by secondary enucleation was performed. Patients with MOKCs who had undergone follow-up for 12 or more months with panoramic radiographs and radiographs of the chest and skull available from the first visit and had been treated by the same team using the same treatment protocol were included in the study. Patients were excluded if the lesion had been treated previously, they had a solitary OKC, or their medical records were not available for review. The treatment methods, recurrence rate, and interval to recurrence were evaluated. The Kaplan-Meier method was used to estimate the survival rate and median time to recurrence. Univariate analysis was used to identify the risk factors associated with recurrence. Significant differences were determined at an α level of 5%. RESULTS: The sample included 81 patients with MOKCs; 21 (25.6%) were male and 60 (74.07%) were female. The age range was 7 to 63 years (mean ± standard deviation, 18.4 ± 4). The overall recurrence rate was 26.63%, with an overall recurrence-free interval of 26.85 months. The average length of follow-up was 55.68 months. No association was found between the treatment method used and the risk of recurrence (P = .178). Although the interval to recurrence was not affected by any of the study variables, the average interval to the recurrence of MOKCs involving the maxilla was short compared with that of MOKCs involving the mandible. CONCLUSIONS: The surgical treatment method did not influence the risk of recurrence in patients with MOKCs, and the interval to recurrence was not associated with any of the study variables.

Lycorine possesses notable anticancer potentials in on-small cell lung carcinoma cells via blocking Wnt/ß-catenin signaling and epithelial-mesenchymal transition (EMT).

Lycorine, an natural isoquinoline alkaloid has reportedly that possesses multi-anticancer activity. However, to date, the anticancer feature of lycorine in non-small cell lung carcinoma (NSCLC) has still not fully been spelled out. The present study mainly focused on the molecular mechanism of lycorine against NSCLC in vitro and vivo. The results showed that lycorine evidently inhibited proliferation of A549 and H460 with IC50 values were 10.83 ± 1.14 µM and 12.35 ± 1.13 µM, while caused slight cytotoxicity in normal pulmonary epithelial Beas-2B cells, and arrested cell cycle in G0/G1 phase. Hoechst DNA-binding staining showed that typical characteristics of nuclear morphology apoptosis, AnnexinV-FITC/PI staining revealed the early-period apoptosis and the dissipation of mitochondrial membrane potential (Δψm) were also captured after lycorine treatment. Moreover, lycorine effectively repressed the Wnt/ß-catenin signaling and reversed epithelial-mesenchymal transition (EMT). In addition, lycorine also intervened the caspase-mediated mitochondrial apoptosis pathway. Furthermore, A549/Luc tumor xenograft model was also corroborated that lycorine significantly suppressed the growth and metastasis of the lung tumor. These data highlight the significance of lycorine as potential anti-neoplastic agents to combat NSCLC.

Lymphotoxins Promote the Progression of Human Lymphatic Malformation by Enhancing Lymphatic Endothelial Cell Proliferation.

Formation of inflammation-related tertiary lymphoid organs promotes human lymphatic malformation (LM) development. However, the role of lymphotoxins (LTs) and LT-related inducible ligand, the crucial mediators for tertiary lymphoid organ formation, is undetermined in LMs. Herein, we show that LTs and LT-related inducible ligand promote LM development by enhancing lymphatic endothelial cell (LEC) proliferation via activating NF-κB pathways. The expression of LTs and their receptors was increased in LMs, especially the infected ones, when compared with normal skins. Nuclear translocation of p65, p52, and RelB in the LECs of LMs indicated the activation of classic and alternative NF-κB pathways. Pearson's correlation and cluster analysis suggested the close relationship between LEC proliferation and NF-κB activation. Moreover, in vitro data demonstrated LTs accelerated the proliferation of human dermal LECs (HdLECs) through activation of NF-κB. In addition, lipopolysaccharide (LPS) up-regulated LT receptor expression in HdLECs, leading to increased sensitivity to LTs. Suppression of LT receptors hampered LPS-enhanced HdLEC proliferation, indicating the crucial role of LT pathways in inflammatory lymphangiogenesis. Besides, evidence from the LM rat models demonstrated LTα and LPS enhanced LEC proliferation, therefore promoting LM development. Blocking LT pathways by neutralizing antibodies against LTα and lymphotoxin ß receptor may decelerate the growth of the disease. In summary, our present study demonstrated activation of LT signaling pathways in LECs contributed to the progression of LMs.

Co3O4 Nanosheets Anchored on SiO2 Nanospheres for Non-Enzymatic Glucose Sensor.

The electrochemical sensing performance is sensitive to the surface area. To achieve superior performance, we design and anchor Co3O4 nanosheets on the surface of SiO2 nanospheres via a simple solvothermal method, which possess large sensing interface and exposed catalytic sites due to the 2D structure and edge terminated feature. Based on these combined structural advantages, the present sample is employed as an ideal platform for non-enzymatic glucose sensing and exhibits high sensitivity, low detection limit, and wide linear range for glucose electrocatalytic oxidation, enabling it as a promising candidate for enzyme-free amperometric sensor for glucose determination.

Glomus tumor in the floor of the mouth: a case report and review of the literature.

BACKGROUND: Glomus tumors are rare benign neoplasms that usually occur in the upper and lower extremities. Oral cavity involvement is exceptionally rare, with only a few cases reported to date. CASE PRESENTATION: A 24-year-old woman with complaints of swelling in the left floor of her mouth for 6 months was referred to our institution. Her swallowing function was slightly affected; however, she did not have pain or tongue paralysis. Enhanced computed tomography revealed a 2.8 × 1.8 × 2.1 cm-sized well-defined, solid, heterogeneous nodule above the mylohyoid muscle. The mandible appeared to be uninvolved. The patient underwent surgery via an intraoral approach; histopathological examination revealed a glomus tumor. The patient has had no evidence of recurrence over 4 years of follow-up. CONCLUSIONS: Glomus tumors should be considered when patients present with painless nodules in the floor of the mouth.

A Double-Lobe Flap Design Combined Nasolabial Advancement and Infraorbital Rotation for Reconstruction of Infraorbital Defect.

Various adjacent flaps have been designed to close infraorbital defect, and each of them is trying to get an aesthetic outcome and meanwhile circumvent eyelid retraction, ectropion, and functional disability. Here, the authors report an adjacent double-lobe flap, which took advantage of nasolabial advancement and infraorbital rotation of the 2 lobes, combinatorially closed a pentagon infraorbital defect by removal of 2 small skin paddles as donor sites, and finally yielded an acceptable aesthetic and functional outcome. This flap may be a new option for closure of polygon infraorbital defects.

Oil-water interfacial behaviour of different caseins and stability of emulsions: Effect of micelle content and caseins concentrations.

This study aimed to investigate the interfacial behaviour of caseins in different micelle content and its effect on the stability of emulsions, including micellar casein concentrate (MCN), calcium caseinate (CaC) and sodium caseinate (NaC). Results revealed that at high protein concentrations (0.5 %-2.5 %), MCN, CaC and NaC exhibited similar interfacial behaviour as well as unfolding rate constants (k 1 ) of 3.11-3.41 × 10-4 (s-1), 2.96-3.35 × 10-4 (s-1) and 2.75-3.27 × 10-4 (s-1), respectively. The interfacial layer formed was dominated by non-micelles, and microscopic images revealed the thickness of the interfacial layer to be 10-20 nm. By contrast, at low concentrations, the differences in the slope of E-π curves and k 1 indicated that the micelle content of casein affects protein interfacial behaviour and properties and that micellar casein is involved in the formation of the interfacial layer. The formation of large numbers of droplets during emulsion preparation results in a similar low concentration environment. Cryo-TEM showed adsorption of micellar casein in all three casein-stabilised emulsions, and the amount of adsorption was proportional to the micelle content. NaC has faster adsorption and rearrangement rates due to fewer micelles and more non-micelles, so that NaC forms smaller droplets and more stable emulsions than those formed by MCN and CaC within the range of 0.5 % to 2.0 %.

A three-dimensional printable conductive composite dressing for accelerating wound healing under electrical stimulation.

In this study, a bioink based on poly(vinyl alcohol) (PVA) and κ-carrageenan network was prepared using conductive polymer (PEDOT:PSS) as conducting medium, and (+)-Catechin-loaded mesoporous ZnO (CmZnO) as antibacterial and anti-inflammatory active medium. 3D conductive composite dressing was further fabricated by an extrusion 3D printing technology. Our results showed that the as-obtained composite dressing had suitable conductivity, efficient blood clotting capacity, and good adhesiveness. It also showed that the as-fabricated conductive composite had 92.9 % and 95.6 % antibacterial activity against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli), respectively. Furthermore, the conductive dressing with an optimal electrical stimulation (ES) parameter showed in vivo blood clotting capacity, and it enhanced in vivo wound healing process in a full-thickness skin defect model than commercial dressings by upregulating the gene expression of growth factors including CD-31 and downregulating inflammatory factor expression of IL-6.