MSI-XGNN: an explainable GNN computational framework integrating transcription- and methylation-level biomarkers for microsatellite instability detection.

Microsatellite instability (MSI) is a hypermutator phenotype caused by DNA mismatch repair deficiency. MSI has been reported in various human cancers, particularly colorectal, gastric and endometrial cancers. MSI is a promising biomarker for cancer prognosis and immune checkpoint blockade immunotherapy. Several computational methods have been developed for MSI detection using DNA- or RNA-based approaches based on next-generation sequencing. Epigenetic mechanisms, such as DNA methylation, regulate gene expression and play critical roles in the development and progression of cancer. We here developed MSI-XGNN, a new computational framework for predicting MSI status using bulk RNA-sequencing and DNA methylation data. MSI-XGNN is an explainable deep learning model that combines a graph neural network (GNN) model to extract features from the gene-methylation probe network with a CatBoost model to classify MSI status. MSI-XGNN, which requires tumor-only samples, exhibited comparable performance with two well-known methods that require tumor-normal paired sequencing data, MSIsensor and MANTIS and better performance than several other tools. MSI-XGNN also showed good generalizability on independent validation datasets. MSI-XGNN identified six MSI markers consisting of four methylation probes (EPM2AIP1|MLH1:cg14598950, EPM2AIP1|MLH1:cg27331401, LNP1:cg05428436 and TSC22D2:cg15048832) and two genes (RPL22L1 and MSH4) constituting the optimal feature subset. All six markers were significantly associated with beneficial tumor microenvironment characteristics for immunotherapy, such as tumor mutation burden, neoantigens and immune checkpoint molecules such as programmed cell death-1 and cytotoxic T-lymphocyte antigen-4. Overall, our study provides a powerful and explainable deep learning model for predicting MSI status and identifying MSI markers that can potentially be used for clinical MSI evaluation.

ASC-expressing pyroptotic extracellular vesicles alleviate sepsis by protecting B cells.

Pyroptosis is an inflammatory programmed cell death process characterized by membrane rupture. Interestingly, pyroptotic cells can generate plenty of nanosized vesicles. Non-inflammatory apoptotic cell death-derived apoptotic vesicles (apoVs) were systemically characterized and displayed multiple physiological functions and therapeutic potentials. However, the characteristics of pyroptotic cell-generated extracellular vesicles (EVs) are largely unknown. Here, we identified a group of pyroptotic EVs (pyroEVs) from in vitro cultured pyroptotic mesenchymal stem cells (MSCs), as well as from septic mouse blood. Compared with apoVs, pyroEVs express similar levels of annexin V, calreticulin, and common EV markers, but express a decreased level of apoptotic marker cleave caspase-3. PyroEVs, but not apoVs and exosomes, specifically express pyroptotic maker apoptosis-associated speck-like protein containing CARD (ASC). More importantly, MSC-derived pyroEVs protect B cells in the spleen and bone marrow to relieve inflammatory responses and enhance the survival rate of the septic mice. Mechanistically, pyroEV membrane-expressed ASC binds to B cells to repress cell death by repressing Toll-like receptor 4. This study uncovered the characteristics of pyroEVs and their therapeutic role in sepsis and B cell-mediated immune response.

A functional study reveals CsNAC086 regulated the biosynthesis of flavonols in Camellia sinensis.

MAIN CONCLUSION: CsNAC086 was found to promote the expression of CsFLS, thus promoting the accumulation of flavonols in Camellia sinensis. Flavonols, the main flavonoids in tea plants, play an important role in the taste and quality of tea. In this study, a NAC TF gene CsNAC086 was isolated from tea plants and confirmed its regulatory role in the expression of flavonol synthase which is a key gene involved in the biosynthesis of flavonols in tea plant. Yeast transcription-activity assays showed that CsNAC086 has self-activation activity. The transcriptional activator domain of CsNAC086 is located in the non-conserved C-terminal region (positions 171-550), while the conserved NAC domain (positions 1-170) does not have self-activation activity. Silencing the CsNAC086 gene using antisense oligonucleotides significantly decreased the expression of CsFLS. As a result, the concentration of flavonols decreased significantly. In overexpressing CsNAC086 tobacco leaves, the expression of NtFLS was significantly increased. Compared with wild-type tobacco, the flavonols concentration increased. Yeast one-hybrid assays showed CsNAC086 did not directly regulate the gene expression of CsFLS. These findings indicate that CsNAC086 plays a role in regulating flavonols biosynthesis in tea plants, which has important implications for selecting and breeding of high-flavonols-concentration containing tea-plant cultivars.

GhRCD1 promotes cotton tolerance to cadmium by regulating the GhbHLH12-GhMYB44-GhHMA1 transcriptional cascade.

Heavy metal pollution poses a significant risk to human health and wreaks havoc on agricultural productivity. Phytoremediation, a plant-based, environmentally benign, and cost-effective method, is employed to remove heavy metals from contaminated soil, particularly in agricultural or heavy metal-sensitive lands. However, the phytoremediation capacity of various plant species and germplasm resources display significant genetic diversity, and the mechanisms underlying these differences remain hitherto obscure. Given its potential benefits, genetic improvement of plants is essential for enhancing their uptake of heavy metals, tolerance to harmful levels, as well as overall growth and development in contaminated soil. In this study, we uncover a molecular cascade that regulates cadmium (Cd2+) tolerance in cotton, involving GhRCD1, GhbHLH12, GhMYB44, and GhHMA1. We identified a Cd2+-sensitive cotton T-DNA insertion mutant with disrupted GhRCD1 expression. Genetic knockout of GhRCD1 by CRISPR/Cas9 technology resulted in reduced Cd2+ tolerance in cotton seedlings, while GhRCD1 overexpression enhanced Cd2+ tolerance. Through molecular interaction studies, we demonstrated that, in response to Cd2+ presence, GhRCD1 directly interacts with GhbHLH12. This interaction activates GhMYB44, which subsequently activates a heavy metal transporter, GhHMA1, by directly binding to a G-box cis-element in its promoter. These findings provide critical insights into a novel GhRCD1-GhbHLH12-GhMYB44-GhHMA1 regulatory module responsible for Cd2+ tolerance in cotton. Furthermore, our study paves the way for the development of elite Cd2+-tolerant cultivars by elucidating the molecular mechanisms governing the genetic control of Cd2+ tolerance in cotton.

Is choroid plexus growth altered in isolated ventriculomegaly on fetal neuro-ultrasound?

OBJECTIVES: Reveal developmental alterations in choroid plexus volume (CPV) among fetuses with isolated ventriculomegaly (VM) through neuro-ultrasound. METHODS: This prospective study aimed to assess the development of fetal CPV in normal fetuses and those with isolated VM through neuro-ultrasound. The fetuses of isolated VM were categorized into mild, moderate, and severe groups, and subsequently, the lateral ventricle evolution was monitored. The developmental alterations in CPV among fetuses with isolated VM were determined by comparing the CPV z-scores with those of normal fetuses. Receiver operating characteristics curve analysis was used to assess the predictive value of altered CPV in lateral ventricle evolution. RESULTS: A total of 218 normal fetuses and 114 isolated VM fetuses from 22 weeks to 35 weeks of gestation were included. The CPV decreased as the isolated VM was getting worse. Both fetuses with isolated moderate ventriculomegaly and those with isolated severe ventriculomegaly exhibited reduced CPV compared to normal fetuses. The CPV in fetuses with isolated mild ventriculomegaly (IMVM) varied, with some showing a larger CPV compared to normal fetuses, while others exhibited a smaller CPV. The larger CPV in cases of IMVM may serve as a predictive factor for either regression or stability of the lateral ventricle, while reduced CPV in cases of isolated VM may indicate worsening of the lateral ventricle. CONCLUSION: The growth volume of fetal CP exhibited alterations in fetuses with isolated VM, and these changes were found to be correlated with the evolution of the lateral ventricle. CLINICAL RELEVANCE STATEMENT: Neuro-ultrasound revealed varying degrees of alterations in the volume development of the choroid plexus within the fetus with isolated VM. The findings can help predict lateral ventricle prognosis, greatly contributing to prenatal diagnosis strategies for fetuses with isolated VM. KEY POINTS: The volume of choroid plexus growth is altered in fetuses with isolated VM. The altered CPV in isolated VM was associated with lateral ventricle evolution. The findings are useful for prenatal counseling and managing fetuses with isolated VM.

LIFU/MMP-2 dual-responsive release of repurposed drug disulfiram from nanodroplets for inhibiting vasculogenic mimicry and lung metastasis in triple-negative breast cancer.

BACKGROUND: Vasculogenic mimicry (VM), when microvascular channels are formed by cancer cells independent of endothelial cells, often occurs in deep hypoxic areas of tumors and contributes to the aggressiveness and metastasis of triple-negative breast cancer (TNBC) cells. However, well-developed VM inhibitors exhibit inadequate efficacy due to their low drug utilization rate and limited deep penetration. Thus, a cost-effective VM inhibition strategy needs to be designed for TNBC treatment. RESULTS: Herein, we designed a low-intensity focused ultrasound (LIFU) and matrix metalloproteinase-2 (MMP-2) dual-responsive nanoplatform termed PFP@PDM-PEG for the cost-effective and efficient utilization of the drug disulfiram (DSF) as a VM inhibitor. The PFP@PDM-PEG nanodroplets effectively penetrated tumors and exhibited substantial accumulation facilitated by PEG deshielding in a LIFU-mediated and MMP-2-sensitive manner. Furthermore, upon exposure to LIFU irradiation, DSF was released controllably under ultrasound imaging guidance. This secure and controllable dual-response DSF delivery platform reduced VM formation by inhibiting COL1/pro-MMP-2 activity, thereby significantly inhibiting tumor progression and metastasis. CONCLUSIONS: Considering the safety of the raw materials, controlled treatment process, and reliable repurposing of DSF, this dual-responsive nanoplatform represents a novel and effective VM-based therapeutic strategy for TNBC in clinical settings.

Highly Sensitive, Portable Detection System for Multiplex Chemiluminescence Analysis.

Chemiluminescence (CL) has emerged as a critical tool for the sensing and quantification of various bioanalytes in virtually all clinical fields. However, the rapid nature of many CL reactions raises challenges for typical low-cost optical sensors such as cameras to achieve accurate and sensitive detection. Meanwhile, classic sensors such as photomultiplier tubes are highly sensitive but lack spatial multiplexing capabilities and are generally not suited for point-of-care applications outside a standard laboratory setting. To address this issue, in this paper, a miniaturized and versatile silicon-photomultiplier-based fiber-integrated CL device (SFCD) was designed for sensitive multiplex CL detection. The SFCD comprises a silicon photomultiplier array coupled to an array of high numerical aperture plastic optical fibers to achieve 16-plex detection. The optical fibers ensure efficient light collection while allowing the fixed detector to be mated with diverse sample geometries (e.g., circular or grid), simply by adjusting the fiber configuration. In a head-to-head comparison with a lens-based camera system featuring a cooled detector, the SFCD achieved a 14-fold improved limit of detection in both direct and enzyme-mediated CL reactions. The SFCD also features improved compactness and lower cost, as well as faster temporal resolution compared with camera-based systems while preserving spatial multiplexing and good environmental robustness. Thus, the SFCD has excellent potential for point-of-care biosensing applications.

GhRCD1 regulates cotton somatic embryogenesis by modulating the GhMYC3-GhMYB44-GhLBD18 transcriptional cascade.

Plant somatic embryogenesis (SE) is a multifactorial developmental process where embryos that can develop into whole plants are produced from somatic cells rather than through the fusion of gametes. The molecular regulation of plant SE, which involves the fate transition of somatic cells into embryogenic cells, is intriguing yet remains elusive. We deciphered the molecular mechanisms by which GhRCD1 interacts with GhMYC3 to regulate cell fate transitions during SE in cotton. While silencing of GhMYC3 had no discernible effect on SE, its overexpression accelerated callus formation, and proliferation. We identified two of GhMYC3 downstream SE regulators, GhMYB44 and GhLBD18. GhMYB44 overexpression was unconducive to callus growth but bolstered EC differentiation. However, GhLBD18 can be triggered by GhMYC3 but inhibited by GhMYB44, which positively regulates callus growth. On top of the regulatory cascade, GhRCD1 antagonistically interacts with GhMYC3 to inhibit the transcriptional function of GhMYC3 on GhMYB44 and GhLBD18, whereby a CRISPR-mediated rcd1 mutation expedites cell fate transition, resembling the effects of GhMYC3 overexpression. Furthermore, we showed that reactive oxygen species (ROS) are involved in SE regulation. Our findings elucidated that SE homeostasis is maintained by the tetrapartite module, GhRCD1-GhMYC3-GhMYB44-GhLBD18, which acts to modulate intracellular ROS in a temporal manner.

Analgesic Effect of Perineural Injection of BoNT/A on Neuropathic Pain Induced by Chronic Constriction Injury of Sciatic Nerve in Rats.

This study was designed to investigate the analgesic effect of perineural injection of BoNT/A on neuropathic pain induced by sciatic nerve chronic constriction injury (CCI) and possible mechanisms. SD rats were randomly divided into Sham group, CCI group and BoNT/A group. Paw mechanical withdrawal threshold (pMWT) and paw thermal withdrawal latency (pTWL) of each group were detected at different time points after surgery. The expression of myelin markers, autophagy markers and NLRP3 inflammasome-related molecules in injured sciatic nerves were examined at 12 days after surgery. Moreover, C-fiber evoked potential in spinal dorsal horn was recorded. The expression of SNAP-25, neuroinflammation and synaptic plasticity in spinal dorsal horn of each group were examined. Then rats treated with BoNT/A were randomly divided into DMSO group and Wnt agonist group to further explore the regulatory effect of BoNT/A on Wnt pathway. We found that pMWT and pTWL of ipsilateral paw were significantly decreased in CCI group compared with Sham group, which could be improved by perineural injection of BoNT/A at days 7, 9 and 12 after surgery. The peripheral analgesic mechanisms of perineural injection of BoNT/A might be related to the protective effect on myelin sheath by inhibiting NLRP3 inflammasome and promoting autophagy flow, while the central analgesic mechanisms might be associated with inhibition of neuroinflammation and synaptic plasticity in spinal dorsal horn due to inhibiting SNAP-25 and Wnt pathway. As a new route of administration, perineural injection of BoNT/A can relieve CCI induced neuropathic pain probably via both peripheral and central analgesic mechanisms.

PD-L1P146R is prognostic and a negative predictor of response to immunotherapy in gastric cancer.

Cancer cells evade immune detection via programmed cell death 1/programmed cell death-ligand 1 (PD-1/PD-L1) interactions that inactivate T cells. PD-1/PD-L1 blockade has become an important therapy in the anti-cancer armamentarium. However, some patients do not benefit from PD-1/PD-L1 blockade despite expressing PD-L1. Here, we screened 101 gastric cancer (GC) patients at diagnosis and 141 healthy control subjects and reported one such subpopulation of GC patients with rs17718883 polymorphism in PD-L1, resulting in a nonsense P146R mutation. We detected rs17718883 in 44% of healthy control subjects, and rs17718883 was associated with a low susceptibility to GC and better prognosis in GC patients. Structural analysis suggests that the mutation weakens the PD-1:PD-L1 interaction. This was supported by co-culture experiments of T cells, with GC cells showing that the P146R substitution results in interferon (IFN)-γ secretion by T cells and enables T cells to suppress GC cell growth. Similar results with animal gastric tumor models were obtained in vivo. PD-1 monoclonal antibody treatment did not enhance the inhibitory effect of T cells on GC cells expressing PD-L1P146Rin vitro or in vivo. This study suggests that rs17718883 is common and may be used as a biomarker for exclusion from PD-1/PD-L1 blockade therapy.

Multiclassifier Radiomics Analysis of Ultrasound for Prediction of Extrathyroidal Extension in Papillary Thyroid Carcinoma in Children.

Objective: To explore extrathyroidal extension (ETE) in children and adolescents with papillary thyroid carcinoma using a multiclassifier ultrasound radiomic model. Methods: In this study, data from 164 pediatric patients with papillary thyroid cancer (PTC) were retrospectively analyzed and patients were randomly divided into a training cohort (115) and a validation cohort (49) in a 7:3 ratio. To extract radiomics features from ultrasound images of the thyroid, areas of interest (ROIs) were delineated layer by layer along the edge of the tumor contour. The feature dimension was then reduced using the correlation coefficient screening method, and 16 features with a nonzero coefficient were chosen using Lasso. Then, in the training cohort, four supervised machine learning radiomics models (k-nearest neighbor, random forest, support vector machine [SVM], and LightGBM) were developed. ROC and decision-making curves were utilized to compare model performance, which was validated using validation cohorts. In addition, the SHapley Additive exPlanations (SHAP) framework was applied to explain the optimal model. Results: In the training cohort, the average area under the curve (AUC) was 0.880 (0.835-0.927), 0.873 (0.829-0.916), 0.999 (0.999-1.000), and 0.926 (0.892-0.926) for the SVM, KNN, random forest, and LightGBM, respectively. In the validation cohort, the AUC for the SVM was 0.784 (0.680-0.889), for the KNN, it was 0.720 (0.615-0.825), for the random forest, it was 0.728 (0.622-0.834), and for the LightGBM, it was 0.832 (0.742-0.921). Generally, the LightGBM model performed well in both the training and validation cohorts. From the SHAP results, original_shape_MinorAxisLength,original_shape_Maximum2DDiameterColumn, and wavelet-HHH_glszm_SmallAreaLowGrayLevelEmphasis have the most significant effect on the model. Conclusions: Our combined model based on machine learning and ultrasonic radiomics demonstrate the excellent predictive ability for extrathyroidal extension (ETE) in pediatric PTC.

Aluminum exposure induces nephrotoxicity via fibrosis and apoptosis through the TGF-ß1/Smads pathway in vivo and in vitro.

Aluminum (Al), the most common element in nature, can enter the body through various routes. Unfortunately, excessive accumulation of Al in the body can cause chronic toxicity. In this study, rats were randomly allocated to 4 groups and intraperitoneally injected with AlCl3 solution at 0, 5, 10, and 20 mg/(kg·d), respectively, for 4 weeks. The kidney function of rats and Al contents in the kidney were measured, and the pathological structural changes and apoptosis of the kidney were observed. Meanwhile, the expression of fibrosis- and apoptosis-related proteins was detected with western blot. For the in vitro assay, HK-2 cells were used to construct a model to evaluate the effects of Al exposure on cell viability, cell apoptosis, and the expression of fibrosis- and apoptosis-related proteins. Additionally, the TGF-ß1/Smads pathway was also altered in HK-2 cells, followed by the measurement of changes in apoptosis and fibrosis-related proteins. The results revealed that Al could accumulate in kidney tissues, then leading to histopathological changes and kidney function impairment, promoting renal tubular cell apoptosis and renal collagen fiber deposition, and also elevating the expression of TGF-ß1/Smads pathway-related proteins. In vitro experiments also exhibited that Al exposure increased apoptosis and the expression of fibrosis-related factors in HK-2 cells, accompanied by activation of the TGF-ß1/Smads pathway. Further modulation of the TGF-ß1/Smads pathway manifested that activation of the TGF-ß1/Smads pathway facilitated Al-induced apoptosis and fibrosis-related factor expression, while inhibition of the pathway negated this effect of Al. In conclusion, the findings of the present study illustrate that Al exposure damages kidney function and facilitate apoptosis and kidney fibrosis, which may be achieved through the activation of the TGF-ß1/Smads pathway. This study provides a new theoretical basis for the study of nephrotoxicity induced by excessive Al exposure.

All-Optical Modulation of Single Defects in Nanodiamonds: Revealing Rotational and Translational Motions in Cell Traction Force Fields.

Measuring the mechanical interplay between cells and their surrounding microenvironment is vital in cell biology and disease diagnosis. Most current methods can only capture the translational motion of fiduciary markers in the deformed matrix, but their rotational motions are normally ignored. Here, by utilizing single nitrogen-vacancy (NV) centers in nanodiamonds (NDs) as fluorescent markers, we propose a linear polarization modulation (LPM) method to monitor in-plane rotational and translational motions of the substrate caused by cell traction forces. Specifically, precise orientation measurement and localization with background suppression were achieved via optical polarization selective excitation of single NV centers with precisions of ∼0.5°/7.5 s and 2 nm/min, respectively. Additionally, we successfully applied this method to monitor the multidimensional movements of NDs attached to the vicinity of cell focal adhesions. The experimental results agreed well with our theoretical calculations, demonstrating the practicability of the NV-based LPM method in studying mechanobiology and cell-material interactions.

Does acupuncture treatment have satisfactory clinical efficacy for late-life depression? A systematic review and meta-analysis.

OBJECTIVE: This systematic review and meta-analysis aimed to assess the clinical efficacy of acupuncture in late-life depression (LLD). METHODS: A comprehensive search of seven electronic databases was conducted from inception to November 2022, including the Cochrane Library, PubMed, Embase, CNKI, VIP, CBM and the Wan Fang database. All data analysis were conducted by Revman 5.3. RESULTS: A total of nine RCTs involving 603 participants were included. The meta-analysis results showed that acupuncture combined with antidepressants significantly reduced HAMD scores (MD, -3.69 [95% CI, -5.11 to -2.27], I2 =74%) and a significantly higher cure rate (RR, 1.11 [95% CI, 1.01 to 1.22], I2 = 0%) compared with antidepressants alone. However, no significant difference was found between acupuncture and antidepressants in reducing HAMD scores and improving clinical outcomes. CONCLUSIONS: Acupuncture combined or not combined with antidepressants is an effective and safe treatment for LLD.

Concentrated growth factor combined with iRoot BP Plus promotes inflamed pulp repair: an in vitro and in vivo study.

BACKGROUND: Platelet concentrates combined with calcium silicate cements may promote reparative dentin formation. However, few studies have reported their effect on dental pulp inflammation. This study aimed to evaluate the effects of concentrated growth factor (CGF) combined with iRoot BP Plus on inflammatory human dental pulp stem cells (hDPSCs) in vitro and inflamed pulp in rats in vivo. METHODS: The proliferation of LPS-stimulated hDPSCs treated with 50% CGF with/without 25% iRoot BP Plus was evaluated using Cell Counting Kit-8 on days 1, 4 and 7. The expression of genes associated with inflammation on day 1 and differentiation on day 14 was analysed by real-time polymerase chain reaction. The exposed pulp of rat maxillary molars was injected with 10 mg/mL LPS and directly capped with CGF membrane with/without iRoot BP Plus extract for 1, 7 and 28 days. The teeth were subjected to histologic analyses and immunohistochemistry. RESULTS: The proliferation rates of the inflammatory hDPSCs after the combination treatment were significantly higher than those after the other treatments on days 4 and 7 (P < 0.05). IL-1ß, IL-6, and TNF-α levels were increased in inflammatory hDPSCs but decreased after treatment with CGF combined with iRoot BP Plus extract, whereas IL-4 and IL-10 showed the opposite expression patterns. Expression of the odontogenesis-related genes OCN, Runx2, and ALP was dramatically enhanced by combined treatment with CGF and iRoot BP Plus extract. In rat pulp, the average inflammation scores of the CGF and CGF-iRoot BP Plus groups significantly decreased in comparison with those of the LPS group (P < 0.05), and the CGF-iRoot BP Plus group had more reparative dentin than the CGF and BP groups. Immunohistochemical staining showed fewer M1 macrophages on day 1 and more M2 macrophages on day 7 in the CGF-iRoot BP Plus group than in the other groups. CONCLUSIONS: The combination of CGF and iRoot BP Plus showed a synergistic effect on anti-inflammatory potential and promoted greater pulp healing than CGF or iRoot BP Plus alone.

Microfluidic Paper-Based Preconcentration and Retrieval for Rapid Ribonucleic Acid Biomarker Detection and Visualization.

Microfluidic paper-based analytical devices (µPADs) have attracted significant attention in the field of point-of-care (POC) diagnostics. However, the heterogeneous structure of the paper often impairs the limit of detection (LOD) for low-abundance targets when those targets are directly analyzed. One viable solution to bypass this limitation is to elevate the target concentration above the LOD on-site to reach a valid readout. Here, we developed a 3D µPADs preconcentrator (3D-µP2) to increase sample concentration by electrokinetic trapping and demonstrated its application in increasing the LOD of a downstream colorimetric assay. The three-dimensional (3D) structure of this device was composed of a loading pad, a vertical fluid path formed by stacked absorbent pads, and an ion-selective membrane of PEDOT:PSS. This novel design facilitates fast preconcentration, high capacity in sample processing, and easy target retrieval. The concentration of an exemplary target, a single-stranded DNA sequence, was increased up to 170-fold within 80 s. The LOD of the colorimetric assay to verify the DNA target was increased 3 orders of magnitude with a preconcentrated sample compared to the control. The device and its analysis equipment used in this study were all cheap and portable. Thus, the 3D-µP2 can be a powerful POC tool for sample pretreatment in resource-limited areas.

Interaction between p53 N terminus and core domain regulates specific and nonspecific DNA binding.

The p53 tumor suppressor is a sequence-specific DNA binding protein that activates gene transcription to regulate cell survival and proliferation. Dynamic control of p53 degradation and DNA binding in response to stress signals are critical for tumor suppression. The p53 N terminus (NT) contains two transactivation domains (TAD1 and TAD2), a proline-rich region (PRR), and multiple phosphorylation sites. Previous work revealed the p53 NT reduced DNA binding in vitro. Here, we show that TAD2 and the PRR inhibit DNA binding by directly interacting with the sequence-specific DNA binding domain (DBD). NMR spectroscopy revealed that TAD2 and the PRR interact with the DBD at or near the DNA binding surface, possibly acting as a nucleic acid mimetic to competitively block DNA binding. In vitro and in vivo DNA binding analyses showed that the NT reduced p53 DNA binding affinity but improved the ability of p53 to distinguish between specific and nonspecific sequences. MDMX inhibits p53 binding to specific target promoters but stimulates binding to nonspecific chromatin sites. The results suggest that the p53 NT regulates the affinity and specificity of DNA binding by the DBD. The p53 NT-interacting proteins and posttranslational modifications may regulate DNA binding, partly by modulating the NT-DBD interaction.

Transcranial color Doppler sonography as an alternative tool for evaluation of terminal internal carotid artery steno-occlusion in moyamoya disease.

OBJECTIVE: To investigate color Doppler ultrasonography criteria and its value in assessing the steno-occlusion of the terminal internal carotid artery in moyamoya disease. METHODS: According to the digital subtraction angiography findings, patients were divided into three groups: occlusion of the terminal internal carotid artery, >50% stenosis, and ≤50% stenosis. We measured the terminal and proximal internal carotid artery parameters of each group using transcranial and cervical color Doppler sonography. RESULTS: Blood flow signals in 12 terminal internal carotid arteries were absent, which were verified as occlusion by digital subtraction angiography. Parameters were obtained in the remaining 159 terminal/proximal internal carotid arteries to predict cutoffs for >50% stenosis and occlusion. For >50% stenosis, mean flow velocity >88.50 cm/s in the terminal internal carotid artery could achieved the highest receiver operating characteristic curve area of 0.776 with 62.50% sensitivity, 88.15% specificity, 48.39% positive predictive values, 92.97% negative predictive value, and 84.27% overall accuracy. For the occlusion, mean flow velocity <49.50 cm/s in the terminal internal carotid artery achieve the highest receiver operating characteristic curve area of 0.734 with 55.56% sensitivity, 83.81% specificity, 63.83% positive predictive values, 78.57% negative predictive value, and 74.21% overall accuracy. The area under receiver operating characteristic curve cutoffs for other parameters were less than 0.7. CONCLUSION: Mean flow velocity of terminal internal carotid artery provides useful diagnostic information for detecting steno-occlusion in moyamoya disease. It may be used as an alternative tool to evaluate steno-occlusion of the terminal internal carotid artery in moyamoya disease.

Impact of agitation/activation strategies on the antibiofilm potential of sodium hypochlorite/etidronate mixture in vitro.

BACKGROUND: To investigate the effect of a rotary agitation method or ultrasonically activated irrigation on the antibiofilm effect of a mixture of sodium hypochlorite (NaOCl) and etidronate (1-hydroxyethylidene-1,1-bisphosphonate, HEBP) using a dual-species biofilm model in root canal system. METHODS: Mature dual-species biofilms of Enterococcus faecalis and Streptococcus gordonii were formed in root canals of mandibular premolars. Teeth were randomly allotted (n = 12) to group 1, XP-endo Finisher (XPF); group 2, ultrasonically activated irrigation (UAI); group 3, syringe-and-needle irrigation (SNI). In all groups, canals were instrumented with a rotary instrument (XP-endo Shaper) prior to irrigant agitation/activation. A mixture containing 2.5% NaOCl and 9% HEBP was used throughout the experiment. Bacterial counts from the canal were determined using qPCR before preparation (S1), after preparation (S2), and after final irrigation agitation/activation (S3). Bacterial viability within the dentinal tubules in the coronal, middle and apical root-thirds was quantified using confocal microscopy after Live/Dead staining. The bacterial counts and viability were compared between groups using one-way ANOVA and post-hoc Tukey's tests. Paired t-test was used to compare the bacterial counts within groups. RESULTS: Instrumentation alone could significantly reduce the microbial counts in all the groups (P < 0.0001). Subsequent agitation/activation resulted in significant microbial reduction only in XPF and UAI (P < 0.05), both of which reduced significantly more microbial counts than SNI (P < 0.05). Live/Dead staining revealed that XPF and UAI showed significantly greater percentage of dead bacteria within the dentinal tubules than SNI in the coronal third (P < 0.05); UAI resulted in the significantly highest percentage of dead bacteria in the middle third (P < 0.05); while there was no significant difference between the groups in the apical third (P > 0.05). CONCLUSIONS: When using the sodium hypochlorite/etidronate mixture for irrigation, final irrigant agitation/activation with XP-endo Finisher or ultrasonic can improve disinfection of the main root canal space and the dentinal tubules in the coronal third, while ultrasonically activated irrigation appears to exhibit better disinfection within dentinal tubules in the middle third.

The miR164-GhCUC2-GhBRC1 module regulates plant architecture through abscisic acid in cotton.

Branching determines cotton architecture and production, but the underlying regulatory mechanisms remain unclear. Here, we report that the miR164-GhCUC2 (CUP-SHAPED COTYLEDON2) module regulates lateral shoot development in cotton and Arabidopsis. We generated OE-GhCUC2m (overexpression GhCUC2m) and STTM164 (short tandem target mimic RNA of miR164) lines in cotton and heterologous expression lines for gh-miR164, GhCUC2 and GhCUC2m in Arabidopsis to study the mechanisms controlling lateral branching. GhCUC2m overexpression resulted in a short-branch phenotype similar to STTM164. In addition, heterologous expression of GhCUC2m led to decreased number and length of branches compared with wild type, opposite to the effects of the OE-gh-pre164 line in Arabidopsis. GhCUC2 interacted with GhBRC1 and exhibited similar negative regulation of branching. Overexpression of GhBRC1 in the brc1-2 mutant partially rescued the mutant phenotype and decreased branch number. GhBRC1 directly bound to the NCED1 promoter and activated its transcription, leading to local abscisic acid (ABA) accumulation and response. Mutation of the NCED1 promoter disrupted activation by GhBRC1. This finding demonstrates a direct relationship between BRC1 and ABA signalling and places ABA downstream of BRC1 in the control of branching development. The miR164-GhCUC2-GhBRC1-GhNCED1 module provides a clear regulatory axis for ABA signalling to control plant architecture.