MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics.

Protein structure prediction is a longstanding issue crucial for identifying new drug targets and providing a mechanistic understanding of protein functions. To enhance the progress in this field, a spectrum of computational methodologies has been cultivated. AlphaFold2 has exhibited exceptional precision in predicting wild-type protein structures, with performance exceeding that of other methods. However, predicting the structures of missense mutant proteins using AlphaFold2 remains challenging due to the intricate and substantial structural alterations caused by minor sequence variations in the mutant proteins. Molecular dynamics (MD) has been validated for precisely capturing changes in amino acid interactions attributed to protein mutations. Therefore, for the first time, a strategy entitled 'MoDAFold' was proposed to improve the accuracy and reliability of missense mutant protein structure prediction by combining AlphaFold2 with MD. Multiple case studies have confirmed the superior performance of MoDAFold compared to other methods, particularly AlphaFold2.

SoCube: an innovative end-to-end doublet detection algorithm for analyzing scRNA-seq data.

Doublets formed during single-cell RNA sequencing (scRNA-seq) severely affect downstream studies, such as differentially expressed gene analysis and cell trajectory inference, and limit the cellular throughput of scRNA-seq. Several doublet detection algorithms are currently available, but their generalization performance could be further improved due to the lack of effective feature-embedding strategies with suitable model architectures. Therefore, SoCube, a novel deep learning algorithm, was developed to precisely detect doublets in various types of scRNA-seq data. SoCube (i) proposed a novel 3D composite feature-embedding strategy that embedded latent gene information and (ii) constructed a multikernel, multichannel CNN-ensembled architecture in conjunction with the feature-embedding strategy. With its excellent performance on benchmark evaluation and several downstream tasks, it is expected to be a powerful algorithm to detect and remove doublets in scRNA-seq data. SoCube is freely provided as an end-to-end tool on the Python official package site PyPi (https://pypi.org/project/socube/) and open-source on GitHub (https://github.com/idrblab/socube/).

A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder.

RNAs play essential roles in diverse physiological and pathological processes by interacting with other molecules (RNA/protein/compound), and various computational methods are available for identifying these interactions. However, the encoding features provided by existing methods are limited and the existing tools does not offer an effective way to integrate the interacting partners. In this study, a task-specific encoding algorithm for RNAs and RNA-associated interactions was therefore developed. This new algorithm was unique in (a) realizing comprehensive RNA feature encoding by introducing a great many of novel features and (b) enabling task-specific integration of interacting partners using convolutional autoencoder-directed feature embedding. Compared with existing methods/tools, this novel algorithm demonstrated superior performances in diverse benchmark testing studies. This algorithm together with its source code could be readily accessed by all user at: https://idrblab.org/corain/ and https://github.com/idrblab/corain/.

microRNA-15a-5p suppresses hypoxia-induced tumor growth and chemoresistance in bladder cancer by binding to eIF5A2.

In various malignant tumors (including bladder cancer) poor prognosis is associated with hypoxia and therapeutic resistance. Evidence indicates that in bladder cancer, microRNAs (miRNAs) have vital functions in acquired drug resistance. However, the involvement of miRNAs in hypoxia-mediated bladder cancer doxorubicin (Dox) resistance is unknown. Herein, we showed that hypoxia and Dox treatment downregulated miR-15a-5p expression. Using UM-UC-3 and J82 bladder cancer cell lines and in vivo mouse models of bladder cancer, we confirmed that miR-15a-5p arrests tumor cell growth and Dox resistance in vitro and in vivo. Furthermore, we determined the interaction between miR-15a-5p and eukaryotic translation initiation factor 5A-2 (eIF5A2) using dual luciferase reporters and quantitative real-time reverse transcription polymerase chain reaction assays. We also showed that a miR-15a-5p agomir repressed EIF5A2 expression in bladder cancer cells, thereby inhibiting the epithelial-mesenchymal transition (EMT) induced by Dox or hypoxia. Moreover, ectopic expression of miR-15a-5p abrogated eIF5A2-mediated Dox resistance in bladder cancer cells. Collectively, these data indicated that hypoxia promotes tumor growth and chemoresistance through the HIF-1α/miR-15a-5p/eIFTA2/EMT pathway. This new finding not only has implications for improving our understanding of the Dox resistance process during bladder cancer progression but also indicates that the miR-15a-5p agomir is a promising tool to prevent Dox resistance in patients with bladder cancer.

Nanomaterial-based biosensors for the detection of foodborne bacteria: a review.

Ensuring food safety is a critical concern for the development and well-being of humanity, as foodborne illnesses caused by foodborne bacteria have increasingly become a major public health concern worldwide. Traditional food safety monitoring systems are expensive and time-consuming, relying heavily on specialized equipment and operations. Therefore, there is an urgent need to develop low-cost, user-friendly and highly sensitive biosensors for detecting foodborne bacteria. In recent years, the combination of nanomaterials with optical biosensors has provided a prospective future platform for the detection of foodborne bacteria. By harnessing the unique properties of nanomaterials, such as their high surface area-to-volume ratio and exceptional sensitivity, in tandem with the precision of optical biosensing techniques, a new prospect has opened up for the rapid and accurate identification of potential bacterial contaminants in food. This review focuses on recent advances and new trends of nanomaterial-based biosensors for the detection of foodborne pathogens, which mainly include noble metal nanoparticles (NMPs), metal organic frameworks (MOFs), graphene nanomaterials, quantum dot (QD) nanomaterials, upconversion fluorescent nanomaterials (UCNPs) and carbon dots (CDs). Additionally, we summarized the research progress of color indicators, nanozymes, natural enzyme vectors and fluorescent dye biosensors, focusing on the advantages and disadvantages of nanomaterial-based biosensors and their development prospects. This review provides an outlook on future technological directions and potential applications to help identify the most promising areas of development in this field.

Lactate-induced mtDNA Accumulation Activates cGAS-STING Signaling and the Inflammatory Response in Sjögren's Syndrome.

Acinar epithelial cell atrophy in secretory glands is a hallmark of primary Sjögren's syndrome (pSS), the cause of which is far from elucidated. We examined the role of acinar atrophy by focusing on the metabolism of glandular epithelial cells and mitochondria in the pSS environment. After confirming the presence of a high-lactate environment in the labial glands of human pSS patients, we used the A253 cell line and NOD/Ltj mice as models to investigate the metabolic changes in salivary gland epithelial cells in a high-lactate environment in vitro and in vivo. We found that epithelial cells produced high levels of IL-6, IL-8, IFN-α, IFN-ß and TNF-α and exhibited significant NF-κB and type I IFN-related pathway activation. The results confirmed that lactate damaged mitochondrial DNA (mtDNA) and led to its leakage, which subsequently activated the cGAS-STING pathway. Inflammatory cytokine production and pathway activation were inhibited in vivo and in vitro by the lactate scavenger sodium dichloroacetate (DCA). Our study provides new insights into the etiology and treatment of pSS from the perspective of cell metabolism.

Sialendoscopy-assisted combined approach for parotid sialolithotomy: Our long-term experience.

OBJECTIVES: To assess the long-term outcome of sialendoscopy-assisted combined approach for parotid sialolithotomy with gland preservation. PATIENTS AND METHODS: A retrospective study of patients treated with a combined sialendoscopic and open approach was conducted between 2011 and 2020. Demographic data of patients such as operative technique, stone size, stone location, complications, and symptom relief were collected. Patients were followed up via clinical examination and questionnaires. RESULTS: Seventy-four patients were included and underwent endoscopy-assisted combined operations for the removal of 98 parotid stones. Of the 98 stones, 92(94%) stones were completely removed and 6(6%) were partially removed. At a mean follow-up of 47.1 ± 35 months, 65 of 74 patients (88%) achieved long-term success. Patients with stone incomplete removal were significantly more often to develop the recurrence of obstructive symptoms (p = 0.000) There were no cases of facial nerve injury or fistula formation. Gland function was preserved in 73 of 74 patients (99%). CONCLUSIONS: The combined approach for parotid stones is a safe and gland-preserving alternative to parotidectomy. The techniques described here show high success rates and good long-term results, and they avoided the need for gland resection in >95% of cases.

The predictive value of laboratory tests in oro-maxillofacial infection of different severity.

OBJECTIVE: We aimed to investigate the value of individual laboratory tests and combinations of tests for predicting disease severity. METHODS: We retrospectively reviewed 62 patients with space infections in the oral and maxillofacial head and neck regions. Patients were divided into three groups according to severity. Laboratory tests associated with disease severity were identified. RESULTS: As the severity of infection increased, leukocytes, neutrophils, C-reactive protein (CRP), procalcitonin (PCT), soluble interleukin receptor (sILR) 2, IL6, and creatinine (CR) increased. In the ROC analysis of group 1 (moderate infection) versus group 2 (severe infection), the area under the curve (AUC) values for leukocytes (AUC = 0.724), neutrophils (AUC = 0.714), PCT (AUC = 0.762) and a combination of the 3 tests (AUC = 0.768) suggested a strong predictive value. Furthermore, in the ROC analysis of group 2 (severe infection) versus group 3 (extremely severe infection), the AUC values for CRP (AUC = 0.84), PCT (AUC = 0.799), sIL2R (AUC = 0.937), IL6 (AUC = 0.863) and a combination of the four tests (AUC = 0.943) suggested a strong predictive value. CONCLUSIONS: Leukocytes, neutrophils, and PCT were associated with multispace infection and high severity. CRP, PCT, sIL2R, and/or IL6 were associated with extremely severe infections occurring in the oral and maxillofacial head and neck regions.

BST-2/Tetherin is involved in BAFF-enhanced proliferation and survival via canonical NF-κB signaling in neoplastic B-lymphoid cells.

The development of Sjögren's syndrome (SS) is accompanied by B cell hyperproliferation and mutation. Our previous study identified aberrant expression of BST-2 (also known as Tetherin/CD317) in B cells from either the peripheral blood or infiltrated salivary glands. However, the roles of BST-2 in the regulation of B cell activation remain unknown. In this study, we identified that BST-2 can respond to BAFF simulation but not to other B cell simulators in neoplastic B cell lines. A CCK-8 assay, an EdU assay and Annexin V/PI staining indicated that BST-2 inhibition attenuated BAFF-enhanced proliferation and survival in both Raji cells and Daudi cells. Screening of BAFF-related signaling in neoplastic B-lymphoid cells indicated that BST-2 was involved in the regulation of NF-κB signaling upon BAFF simulation. However, inhibition of NF-κB by JSH-23 significantly reduced the proliferation and survival of Raji and Daudi cells under both normal and BAFF-simulated conditions. Collectively, our results indicate that BST-2/Tetherin is a BAFF-responsive membrane factor involved in the regulation of NF-κB signaling, thereby assisting in the proliferation and survival of neoplastic B-lymphoid cells. Our study provides a potential molecular mechanism underlying aberrant overactivation of B cells upon SS development.

Accumulation of RIPK1 into mitochondria is requisite for oxidative stress-mediated necroptosis and proliferation in Rat Schwann cells.

The injury of Schwann cells is an important pathological feature of peripheral neuropathy. However, the explicit molecular mechanism and blocking method remains to be explored. In this study, we identified an pivotal executor of necroptosis-RIPK1, performed an unique function in response to oxidative stress-induced injury in Rat Schwann cells. We found that after oxidative stress-simulation by H2O2, RIPK1 was activated independent of genetic up-regulation, but through the post-translational modification, including its protein levels, phosphorylation of Serine 166 and Serine 321 sites and its general ubiquitination levels. Under a confocal microscopy, we found that RIPK1 was significantly accumulated into the mitochondria. And the phosphorylation, ubiquitination levels were also elevated in mitochondrial RIPK1, as indicated by immunoprecipitation. Through the administration of N-Acetyl-L-cysteine (NAC), a ROS inhibitor, we found that the phosphorylation, ubiquitination and mitochondrial location of RIPK1 was significantly suppressed. While administration of Necrostatin-1 (Nec-1) failed to influence the levels of ROS and mitochondrial membrane potential, revealing that RIPK1 served as the down-stream regulators of ROS. Lastly, pharmacological inhibition of RIPK1 by Nec-1 attenuated the levels of necroptosis, increased proliferation, as indicated by Annexin V/PI evaluation, CCK-8 detection, TEM scanning and EdU staining. Our results indicate a previous un-recognized post-translational change of RIPK1 in response to oxidative stress in Schwann cells.

Efficacy of needle aspiration in patients with oral-maxillofacial abscesses: A retrospective study of 15 consecutive patients.

The aim of this study was to determine the adequacy and safety of needle aspiration (NA) as an alternative to open surgical drainage for oral-maxillofacial abscesses. Fifteen consecutive patients who were diagnosed with oral-maxillofacial abscesses via contrast-enhanced CT from January 2020 to December 2020 were included. All patients were on antibiotics and treated with NA under local anaesthesia using a 20 mL syringe. Data collection included patient characteristics, signs and symptoms, physical examinations, laboratory tests, imaging findings, and outcomes. Next-generation sequencing (NGS) was used to identify the infectious microorganisms from the abscess samples. The study included 15 patients with oral-maxillofacial abscesses. None of our 15 patients required surgical incision and drainage, although repeat aspiration was required. However, after the first NA, the pain was reportedly extremely relieved for all patients. The average duration of antibiotic treatment was 9.20 ± 5.15 days (range 4-23 days). The abscess-affected spaces mainly included the masseter space and submandibular space. Odontogenic infection was the most common aetiology in 15 patients (10/15). The average volume of the abscesses on CT was 5866.26 ± 3627.18 mm3. The main pathogens identified in this study were Prevotella oris (5/15), Peptostreptococcus stomatis (4/15) and Porphyromonas endodontalis (2/15). According to the results of our study, the data support the use of NA as an effective, minimally invasive treatment modality for oral-maxillofacial abscesses. Surgeons should familiarise themselves with this technique, as it can easily be performed in the clinic using local anaesthesia, culture samples may be obtained, and airway obstruction and pain may be relieved.

Prediction of 3-month treatment outcome of IgG4-DS based on BP artificial neural network.

OBJECTIVE: The study aimed to establish an effective back-Propagation artificial neural network (BP-ANN) model for automatic prediction of 3-month treatment outcome of IgG4-DS. METHODS: A total of 26 IgG4-DS patients at Shanghai Ninth People's Hospital from January 2018 to December 2019 were involved in the study. They were all followed for >3 months. The primary outcome was reduction of serum IgG4 (sIgG4) after 3-month treatment. The association between risk factors and reduction of sIgG4 was analyzed by Spearman's rank correlation test. According to the R values, we built a BP-ANN model by MATLAB R2019b. RESULTS: The average reduction of sIgG4 was 5.55 ± 5.03. After Spearman's rank correlation test, ESR, sIgG4, and sIgG were independently associated with reduction of sIgG4 (p < .05) and were selected as input variables. Take into account these parameters, BP-ANN model was developed and the coefficient of determination (R2 ) model was 0.95512. CONCLUSION: The BP-ANN model based on ESR, sIgG4, and sIgG could predict the 3-month reduction of sIgG4 for IgG4-DS patients. It showed potential clinical application value.

Evaluation of chromosomal abnormalities from preimplantation genetic testing to the reproductive outcomes: a comparison between three different structural rearrangements based on next-generation sequencing.

PURPOSE: The aim of this study was to determine factors affecting the chromosome imbalance in blastocysts and reproductive outcomes by a comparison between the reciprocal translocation (REC), inversion (INV), and Robertsonian translocation (ROB) carriers. METHODS: Couples with one partner carrying translocation or inversion underwent preimplantation genetic testing for chromosomal structural rearrangement (PGT-SR) cycles, including 215 PGT-SR cycles performed in subsequent 164 frozen-thawed embryo transfer cycles and 61 prenatal diagnoses of fetuses and 59 normal live birth babies. A total of 899 samples were processed by whole-genome amplification followed by next-generation sequencing (NGS). Karyotype and chromosome microarray analyses were used to confirm the PGT results from the amniotic fluid samples. RESULTS: A total of 843 blastocysts from 124 REC, 21 INV, and 35 ROB carriers were diagnosed by PGT-SR. The percentage of unbalanced blastocysts was significantly higher in REC than in INV and ROB carriers (64.31% vs. 28.05% vs. 37.02%). Stratification analysis of female carrier age and gonadotropin doses showed no significant increase in unbalanced chromosomal abnormalities in the three groups. Also, the different breakpoints in chromosomal arms did not affect the rate of unbalanced chromosomes in the embryos. Logistic regression indicated blastocyst quality as a statistically significant risk factor associated with unbalanced chromosomal abnormalities from translocation carriers (P < 0.001). The source of abnormalities in the three groups showed significant differences such that the abnormalities in REC mostly originated from parental translocation but the abnormalities in INV were mainly de novo variations. 164 blastocysts were transferred, and there were no significant differences in the clinical pregnancy rate and miscarriage rate. A total of 59 healthy babies were born, and there were no significant differences in the gender ratio and birth height, except the birth weight of boys between INV and ROB groups (P = 0.02). The results of amniocentesis revealed that more fetuses have normal chromosomal karyotypes than balanced carriers, particularly in the REC group. CONCLUSIONS: Reciprocal translocation carriers have more risk of unbalanced rearrangement, but embryonic chromosome abnormalities of inversion carriers come mainly from de novo variations. This is the first study specifically comparing three different PGT-SRs using the NGS method and evaluating their reproductive outcomes. Our findings will provide the reciprocal translocation, inversion, and Robertsonian translocation carrier couples with more accurate genetic counseling on the reproductive risk of chromosomal imbalance.

Prepupae and pupae transcriptomic characterization of Trichogramma chilonis.

The egg parasitoid, Trichogramma chilonis, has significant control effects on agriculture and forestry pests and is widely employed in southern China for the biological control of lepidopteran pests. In this study, transcriptomic analysis was used to gain a clear understanding of the molecular changes in prepupae and pupae of T. chilonis. A total of 16.88 Gb of clean data were obtained and finally assembled into 43,136 unigenes, 18,880 of which were annotated. After FPKM standardization, 117 and 838 specific expression genes were found in prepupae and pupae, respectively. There were 3129 differentially expressed genes between prepupae and pupae. Compared to pupae, 806 genes were up-regulated and 2323 were down-regulated in prepupae. Background on the T. chilonis transcriptome, the enriched GO function and KEGG pathway analysis of DEGs were considered. As indicated by GO classification, up-regulated genes were mainly involved in chitin metabolism, cell adhesion and endocytic, while most down-regulated genes were involved in synthesis of cell components, ion transport and biological regulation. KEGG enrichment analysis showed that 458 DEGs were enriched in 94 metabolic pathways. DEGs involved in nucleotide replication and transcription, substance metabolism, insect hormone biosynthesis, cell growth and death, reproductive metabolism, circadian rhythms and signal transduction pathways were up-regulated or down-regulated to different degrees, indicating that these genes played important roles during the process of metamorphosis in T. chilonis. This study provides a rich data source for the future study of T. chilonis molecular and biological mechanisms. A large number of genes related to metamorphosis were found based on comparison analysis between prepupae and pupae transcriptomes. This study lays a good foundation for in-depth study of gene transcription and regulation mechanisms during T. chilonis metamorphosis.

LncRNA PVT1 links Myc to glycolytic metabolism upon CD4+ T cell activation and Sjögren's syndrome-like autoimmune response.

The hyperproliferation and hyperactivation of CD4+ T cells in salivary gland tissue is a hallmark of Sjögren's syndrome (SS). However, the role of long noncoding RNAs (lncRNAs) in the pathological process of SS and CD4+ T cell activation has not been fully elucidated. Here, we reported that lncRNA PVT1 was involved in the glycolytic metabolism reprogramming and proliferation upon CD4+ T cell activation. Expression of PVT1 was positively related with CD4+ T cell activation both in SS patients and Ex vivo antigen simulation. Depletion of PVT1 decreased the proliferation of murine CD4+ T cells and Jurkat T cells upon activation. We also showed that expression of the transcription factor Myc is regulated by PVT1 under antigen simulation. Depletion of PVT1 significantly decreased the expression of glycolytic genes, as well as several pivotal glycolytic proteins that were directly transcribed by Myc. Measurement of glucose content and lactate secretion indicated a defected lactate secretion and glucose uptake in PVT1-depleted T cells. Additionally, the real-time extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) measurement also affirmed that PVT1 maintains glycolytic levels, glycolytic capacity under stress and ECAR/OCR ratios during T cell activation. Polarizing assays indicate that PVT1 depletion defected the function of Th1 effector cells as well as down-regulated Myc expression and glycolytic levels. Furthermore, we observed increased glycolytic levels in CD4+ T cells from SS-like NOD/Ltj mice. Treatment with 2-deoxy-d-glucose (2-DG), an inhibitor of glycolysis, significantly decreased the extent of lymphocyte infiltration and CD4+ T cell numbers and attenuated the defect of salivary flow in the lesioned submandibular glands of NOD/Ltj mice. Thus, our study demonstrated that lncRNA PVT1, which was upregulated in the CD4+T cells of SS patients, could maintain the expression of Myc, thus controlling the proliferation and effector functions of CD4+ T cells through regulating the reprogramming of glycolysis. Inhibition of glycolysis could attenuate the proliferation of CD4+ T cells and the SS-like autoimmune response. Our study provides a novel mechanistic function of lncRNA PVT1 in the pathogenesis of SS.

Dysregulated interleukin 11 in primary Sjögren's syndrome contributes to apoptosis of glandular epithelial cells.

The purpose of this study was to explore the potential function of interleukin-11 (IL-11) in the pathogenesis of primary Sjögren's syndrome (pSS) patients. Real-time polymerase chain reaction was performed to examine IL-11 expression in the labial glands of 30 pSS patients and 30 healthy controls. Immunohistochemistry was conducted to assess the distribution of IL-ll-positive cells in labial glands. The human salivary gland (HSG) cell line was used to study the effects of IL-11 on gland epithelial cells in vitro. Cell viability and cell proliferation were examined by CCK-8 kit and EdU assay, respectively. The population of apoptotic cells was detected in flow cytometry followed by Annexin V/PI and Hoechst staining. We found that the expression levels of IL-11 were remarkably decreased in pSS labial glands and were positively correlated with C-reactive protein levels and negatively correlated with rheumatoid factor levels. Fewer numbers of glandular epithelial cells were observed to be positively stained with IL-11 antibody in labial glands from pSS patients than those in healthy control patients. After IL-11 treatment, the viability and proliferation of HSG cells were significantly higher than those in the control group. The total apoptotic and necrotic rates of HSG cells in the group after IL-11 treatment were significantly lower. In conclusion, the results indicated that IL-11 promoted viability and proliferation and inhibited apoptotic and necrotic rates of glandular epithelial cells. In pSS, downregulated IL-11 might contribute to the apoptosis of salivary gland epithelial cells. However, it might be a potential target to alleviate the pathological atrophy of glandular epithelial cells in pSS patients.

Toll-like receptor 9 signaling promotes autophagy and apoptosis via divergent functions of the p38/JNK pathway in human salivary gland cells.

Abnormal signaling transduction in salivary gland cells is associated with the pathogenesis of Sjögren's syndrome (SS). Previously, we identified aberrant expression of toll-like receptor 9 (TLR9) in gland cells of SS patients and mouse models. In this study, we investigated the role of TLR9 and its downstream p38/mitogen-activated protein kinase (MAPK) and c-Jun N-terminal kinase (JNK) signaling in mediating apoptosis and autophagy in human salivary gland (HSG) cells. We selected either CpG-Odn, a classical TLR9 activator, or lentivirus-packaged TLR9 full-length cDNA to activate TLR9 signaling transduction. Activation of TLR9 signaling induced phosphorylation of its downstream protein kinases, p38/MAPK and JNK, in a time-dependent manner, and decreased HSG cell viability. Western blotting of LC3B-II and p62 in both normal and autophagic flux-administered conditions revealed elevated autophagy upon TLR9 activation. Observing the cell cytoplasm through transmission electron microscopy and mRFP-GFP-LC3B-tagged fluorescence confirmed an increased number of autophagosomes and autolysosomes in TLR9-activated cells. Bax/Bcl-2 ratio calculations, caspase-3 activity assays and Hoechst nuclear staining were utilized to confirm the involvement of apoptosis in TLR9 signaling activation. Furthermore, we selected SB239063, a p38/MAPK signaling inhibitor, and SP600125, a JNK inhibitor, to identify the functions of p38/MAPK and JNK in TLR9-mediated signaling transduction. Multiple approaches, including Western blotting assays, fluorescence assessments and caspase-3 activity measurements, confirmed that inhibition of p38/MAPK signaling ameliorated both autophagy and apoptosis in TLR9-activated HSG cells, whereas inhibition of JNK signaling attenuated apoptosis but failed to modulate autophagy in the models mentioned above. Our results indicate a divergent function of p38/MAPK and JNK in TLR9-mediated autophagy and apoptosis in salivary gland cells.

A whole-genome sequencing-based novel preimplantation genetic testing method for de novo mutations combined with chromosomal balanced translocations.

PURPOSE: To explore a new preimplantation genetic testing (PGT) method for de novo mutations (DNMs) combined with chromosomal balanced translocations by whole-genome sequencing (WGS) using the MGISEQ-2000 sequencer. METHODS: Two families, one with maternal Olmsted syndrome caused by DNM (c.1246C>T) in TRPV3 and a paternal Robertsonian translocation and one with paternal Marfan syndrome caused by DNM (c.4952_4955delAATG) in FBN1 and a maternal reciprocal translocation, underwent PGT for monogenetic disease (PGT-M), chromosomal aneuploidy, and structural rearrangement. WGS of embryos and family members were performed. Bioinformatics analysis based on gradient sequencing depth was performed, and parent-embryo haplotyping was conducted for DNM diagnosis. Sanger sequencing, karyotyping, and chromosomal microarray analysis were performed using an amniotic fluid sample to confirm the PGT results. RESULTS: After 1 PGT cycle, WGS of 2 embryos from the Olmsted syndrome family revealed euploid embryos without DNMs; after 2 cycles, the 11 embryos from the Marfan syndrome family showed only 1 normal embryo without DNM, copy number variations (CNVs), or aneuploidy. Moreover, 1 blastocyst from the Marfan syndrome family was transferred back to the uterus; the amniocentesis test results were confirmed by PGT and a healthy infant was born. CONCLUSIONS: WGS based on parent-embryo haplotypes was an effective strategy for PGT of DNMs combined with a chromosomal balanced translocation. Our results indicate this is a reliable and effective diagnostic method that is useful for clinical application in PGT of patients with DNMs.

A colorimetric immunosensor for determination of foodborne bacteria using rotating immunomagnetic separation, gold nanorod indication, and click chemistry amplification.

A colorimetric immunosensor was developed for the determination of Salmonella Typhimurium using rotating magnetic separation, gold nanorod (GNR) indication, and click chemistry amplification. The target bacteria were first separated from large-volume sample using a rotating magnetic field and a small amount (50 µg) of immunomagnetic nanoparticles (MNPs), resulting in the forming of magnetic bacteria. Then, the magnetic bacteria were conjugated with catalase (CAT)-labeled antibodies, which were synthesized using trans-cyclooctene/1,2,4,5-tetrazine click chemistry reaction, resulting in the forming of enzymatic bacteria. Then the CATs on the enzymatic bacteria were used to decompose an excessive amount of hydrogen peroxide (H2O2), the remaining H2O2 was mixed with horseradish peroxidase to etch the GNRs, resulting in color change and absorbance peak shift of the GNRs. Finally, the peak shift was measured and analyzed for the quantitative determination of target bacteria. This immunosensor was able to detect Salmonella Typhimurium with a linear range of 101-105 CFU mL-1 in 3 h with a low detection limit of 35 CFU mL-1. The mean recovery for Salmonella Typhimurium in spiked chicken samples was 109%. Graphical abstractSchematic representation of a colorimetric immunosensor for the determination of Salmonella Typhimurium as low as 35 CFU mL-1 using rotating magnetic separation of Salmonella from a large-volume sample, click chemistry reaction of catalase with antibodies for signal amplification, and HRP-mediated gold nanorod etching for result indication.

A Rapid and Sensitive Salmonella Biosensor Based on Viscoelastic Inertial Microfluidics.

Salmonella is a main cause of foodborne illnesses and rapid screening of Salmonella is the key to prevent Salmonella outbreaks, however available detection methods either require a long time, or need complex pretreatment, or have low sensitivity. In this study, a microfluidic biosensor was developed for Salmonella detection using viscoelastic inertial microfluidics for separating magnetic bacteria from unbound magnetic nanoparticles (MNPs) and enzyme catalytic colorimetry for amplifying biological signals. The polyclonal antibodies and horseradish peroxidase (HRP) modified MNPs were first used to specifically capture Salmonella to form magnetic HRP-bacteria. Both magnetic HRP-bacteria and unbound MNPs were magnetically separated from background and resuspended in viscoelastic polyvinylpyrrolidone solution as sample flow. When sample flow was injected with polyvinylpyrrolidone sheath flow into a T-shaped microchannel, larger-sized magnetic HRP-bacteria could penetrate the sample flow, however smaller-sized MNPs remained in the sample flow due to weaker inertial lift force and elastic lift force, resulting in continuous-flow separation of magnetic HRP-bacteria. Finally, magnetic HRP-bacteria were collected and concentrated to catalyze tetramethyl benzidine, and absorbance was measured to determine the bacteria. This biosensor was able to detect Salmonella as low as 30 CFU/mL in 1 h and featured the advantages of shorter time due to a one-step immunoreaction, easier extension due to only one antibody and one label, and lower cost due to less expensive materials.