The ECG abnormalities in persons with chronic disorders of consciousness.

We aimed to investigate the electrocardiogram (ECG) features in persons with chronic disorders of consciousness (DOC, ≥ 29 days since injury, DSI) resulted from the most severe brain damages. The ECG data from 30 patients with chronic DOC and 18 healthy controls (HCs) were recorded during resting wakefulness state for about five minutes. The patients were classified into vegetative state (VS) and minimally conscious state (MCS). Eight ECG metrics were extracted for comparisons between the subject subgroups, and regression analysis of the metrics were conducted on the DSI (29-593 days). The DOC patients exhibit a significantly higher heart rate (HR, p = 0.009) and lower values for SDNN (p = 0.001), CVRR (p = 0.009), and T-wave amplitude (p < 0.001) compared to the HCs. However, there're no significant differences in QRS, QT, QTc, or ST amplitude between the two groups (p > 0.05). Three ECG metrics of the DOC patients-HR, SDNN, and CVRR-are significantly correlated with the DSI. The ECG abnormalities persist in chronic DOC patients. The abnormalities are mainly manifested in the rhythm features HR, SDNN and CVRR, but not the waveform features such as QRS width, QT, QTc, ST and T-wave amplitudes.

Alpha anteriorization and theta posteriorization during deep sleep.

Brain states (wake, sleep, general anesthesia, etc.) are profoundly associated with the spatiotemporal dynamics of brain oscillations. Previous studies showed that the EEG alpha power shifted from the occipital cortex to the frontal cortex (alpha anteriorization) after being induced into a state of general anesthesia via propofol. The sleep research literature suggests that slow waves and sleep spindles are generated locally and propagated gradually to different brain regions. Since sleep and general anesthesia are conceptualized under the same framework of consciousness, the present study examines whether alpha anteriorization similarly occurs during sleep and how the EEG power in other frequency bands changes during different sleep stages. The results from the analysis of three polysomnography datasets of 234 participants show consistent alpha anteriorization during the sleep stages N2 and N3, beta anteriorization during stage REM, and theta posteriorization during stages N2 and N3. Although it is known that the neural circuits responsible for sleep are not exactly the same for general anesthesia, the findings of alpha anteriorization in this study suggest that, at macro level, the circuits for alpha oscillations are organized in the similar cortical areas. The spatial shifts of EEG power in different frequency bands during sleep may offer meaningful neurophysiological markers for the level of consciousness.

Genome-wide analysis of the peanut CaM/CML gene family reveals that the AhCML69 gene is associated with resistance to Ralstonia solanacearum.

BACKGROUND: Calmodulins (CaMs)/CaM-like proteins (CMLs) are crucial Ca2+-binding sensors that can decode and transduce Ca2+ signals during plant development and in response to various stimuli. The CaM/CML gene family has been characterized in many plant species, but this family has not yet been characterized and analyzed in peanut, especially for its functions in response to Ralstonia solanacearum. In this study, we performed a genome-wide analysis to analyze the CaM/CML genes and their functions in resistance to R. solanacearum. RESULTS: Here, 67, 72, and 214 CaM/CML genes were identified from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively. The genes were divided into nine subgroups (Groups I-IX) with relatively conserved exon‒intron structures and motif compositions. Gene duplication, which included whole-genome duplication, tandem repeats, scattered repeats, and unconnected repeats, produced approximately 81 pairs of homologous genes in the AhCaM/CML gene family. Allopolyploidization was the main reason for the greater number of AhCaM/CML members. The nonsynonymous (Ka) versus synonymous (Ks) substitution rates (less than 1.0) suggested that all homologous pairs underwent intensive purifying selection pressure during evolution. AhCML69 was constitutively expressed in different tissues of peanut plants and was involved in the response to R. solanacearum infection. The AhCML69 protein was localized in the cytoplasm and nucleus. Transient overexpression of AhCML69 in tobacco leaves increased resistance to R. solanacearum infection and induced the expression of defense-related genes, suggesting that AhCML69 is a positive regulator of disease resistance. CONCLUSIONS: This study provides the first comprehensive analysis of the AhCaM/CML gene family and potential genetic resources for the molecular design and breeding of peanut bacterial wilt resistance.

Predictive value of monocyte to high-density lipoprotein cholesterol ratio and tumor markers in colorectal cancer and their relationship with clinicopathological characteristics.

OBJECTIVE: To evaluate the predictive value of monocyte (M) to high-density lipoprotein cholesterol (HDL-C) ratio (MHR) and tumor markers in colorectal cancer (CRC) and their correlation with clinicopathological characteristics. METHODS: Hematology test data and medical records of 202 CRC patients and 201 healthy subjects were collected retrospectively. The diagnostic efficacy of MHR was evaluated using receiver operating characteristic (ROC) curves and risk factors for CRC were analyzed by multivariate logistic regression. RESULTS: CRC patients had significantly higher M, MHR, carcinoembryonic antigen (CEA), and carbohydrate antigen 199 (CA199) levels, but significantly lower HDL-C levels than healthy controls (all P < 0.05). Additionally, MHR was positively correlated with tumor differentiation in CRC patients (P = 0.049); CEA and CA199 levels in CRC patients increased with increased stage, lymph node metastasis and tumor size ≥ 5 cm (all P < 0.05). Furthermore, high levels of MHR, CA199 and CEA were independent risk factors for CRC. The area under ROC curve of MHR combined with CEA and CA199 was 0.882/0.869 for the diagnosis of CRC, respectively. CONCLUSION: This is the first study to explore the predictive value of MHR in CRC, and its continuous increase is an independent risk factor for CRC. MHR is a promising predictor for CRC progression along with CA199 and CEA.

LAPTM4B-YAP loop feedback amplification enhances the stemness of hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is highly heterogeneous, and stemness signatures are frequently elevated in HCC tumor cells to generate heterogeneous subtypes via multidirectional differentiation. However, the mechanisms affecting the regulation of stemness in HCC remain unclear. In this study, we identified that lysosome-associated protein transmembrane-4ß (LAPTM4B) was significantly overexpressed in stem-like tumor cell populations with multidirectional differentiation potential at the single cell level, and verified that LAPTM4B was closely related to stemness of HCC using in vitro and in vivo experiments. Mechanistically, elevated LAPTM4B suppresses Yes-associated protein (YAP) phosphorylation and ubiquitination degradation. In turn, stabilized YAP localizes to the nucleus and binds to cAMP responsive element binding protein-1 (CREB1), which promotes transcription of LAPTM4B. Overall, our findings suggest that LAPTM4B forms a positive feedback loop with YAP, which maintains the stemness of HCC tumor cells and leads to an unfavorable prognosis for HCC patients.

Protein phosphatase StTOPP6 negatively regulates potato bacterial wilt resistance by modulating MAPK signaling.

Potato (Solanum tuberosum) is an important crop globally and is grown across many regions in China, where it ranks fourth in the list of staple foods. However, its production and quality are severely affected by bacterial wilt caused by Ralstonia solanacearum. In this study, we identified StTOPP6, which belongs to the type one protein phosphatase (TOPP) family, and found that transient knock down of StTOPP6 in potato increased resistance against R. solanacearum. RNA-seq analysis showed that knock down of StTOPP6 activated immune responses, and this defense activation partly depended on the mitogen-activated protein kinase (MAPK) signal pathway. StTOPP6 inhibited the expression of StMAPK3, while overexpression of StMAPK3 enhanced resistance to R. solanacearum, supporting the negative role of StTOPP6 in plant immunity. Consistent with the results of knock down of StTOPP6, overexpressing the phosphatase-dead mutation StTOPP6m also attenuated infection and up-regulated MAPK3, showing that StTOPP6 activity is required for disease. Furthermore, we found that StTOPP6 affected the StMAPK3-mediated downstream defense pathway, eventually suppressing the accumulation of reactive oxygen species (ROS). Consistent with these findings, plants with knock down of StTOPP6, overexpression of StTOPP6m, and overexpression of StMAPK3 all displayed ROS accumulation and enhanced resistance to R. solanacearum. Taken together, the findings of our study demonstrate that StTOPP6 negatively regulates resistance to bacterial wilt by affecting the MAPK3-mediated pathway.

Comparative genomic analysis of Ralstonia solanacearum reveals candidate avirulence effectors in HA4-1 triggering wild potato immunity.

Ralstonia solanacearum is the causal agent of potato bacterial wilt, a major potato bacterial disease. Among the pathogenicity determinants, the Type III Secretion System Effectors (T3Es) play a vital role in the interaction. Investigating the avirulent T3Es recognized by host resistance proteins is an effective method to uncover the resistance mechanism of potato against R. solanacearum. Two closely related R. solanacearum strains HA4-1 and HZAU091 were found to be avirulent and highly virulent to the wild potato Solanum albicans 28-1, respectively. The complete genome of HZAU091 was sequenced in this study. HZAU091 and HA4-1 shared over 99.9% nucleotide identity with each other. Comparing genomics of closely related strains provides deeper insights into the interaction between hosts and pathogens, especially the mechanism of virulence. The comparison of type III effector repertoires between HA4-1 and HZAU091 uncovered seven distinct effectors. Two predicted effectors RipA5 and the novel effector RipBS in HA4-1 could significantly reduce the virulence of HZAU091 when they were transformed into HZAU091. Furthermore, the pathogenicity assays of mutated strains HA4-1 ΔRipS6, HA4-1 ΔRipO1, HA4-1 ΔRipBS, and HA4-1 ΔHyp6 uncovered that the absence of these T3Es enhanced the HA4-1 virulence to wild potato S. albicans 28-1. This result indicated that these T3Es may be recognized by S. albicans 28-1 as avirulence proteins to trigger the resistance. In summary, this study provides a foundation to unravel the R. solanacearum-potato interaction and facilitates the development of resistance potato against bacterial wilt.

Evaluation of Copper Levels in Dental Calculus of OSF Patients with Chewing Dried Areca-Nut Quids in Hunan Province of Mainland China.

Dental calculus is a potential material that can be used for assessing chronic exposure to trace heavy metals in oral cavity as it is a long-term reservoir. The aim of this study was to investigate the correlation between dental calculus copper levels and risk of oral submucous fibrosis (OSF) due to chewing dried areca-nut quids in Mainland China. This study included 34 OSF (grade 1) sufferers with dried areca-nut quids chewing as the patient group and 23 healthy individuals without areca-nut chewing as the control group. The dental calculus sample was obtained from all 57 participants and evaluated by inductively coupled plasma mass spectrometry (ICP-MS) for dental calculus level of copper. This work revealed that the mean copper level of dental calculus was significantly higher in OSF (grade 1) sufferers with areca-nut chewing than those in healthy individuals without areca-nut chewing (p < 0.001). This work provided an evidence to support that there may be a positive correlation between elevated levels of copper in dental calculus caused by chewing dried areca-nut quids and an increased risk of developing OSF in Mainland China.

Inhibition of the B7-H3 immune checkpoint limits hepatocellular carcinoma progression by enhancing T lymphocyte-mediated immune cytotoxicity in vitro and in vivo.

PURPOSE: The interaction between tumor cells and immune system in hepatocellular carcinoma (HCC) remains unclear. Great clinical achievements have progressed in HCC patients treated with immune checkpoint inhibitors (ICIs) for programmed death-1 and its ligands. However, response efficacy for these therapies is limited, thereby requiring alternative ICI candidates for HCC treatment. B7 homolog 3 protein (B7-H3), an immunoregulatory protein, plays a significant role in tumor immunity and disease progression. In this study, we evaluated the correlation between B7-H3 expression and prognosis of HCC patients, and investigated the therapeutic potential of B7-H3 targeting in HCC. METHODS: B7-H3 expression was analyzed immunohistochemically in HCC patients, and its relationship with tumor-infiltrating lymphocyte infiltration was assessed. The anti-tumor efficacy of anti-B7-H3 antibody therapy was determined using an in vitro co-culture system and a subcutaneous HCC-bearing murine model. RESULTS: We found that B7-H3 overexpressed in tumor cells and positively correlated with poor prognosis in HCC patients. B7-H3 inhibited the infiltration of CD8+ T cells in tumors. Furthermore, co-culture experiment indicated that inhibiting B7-H3 in tumor cells significantly increased T cells-mediated immune activities and tumor cell killing. Consistently, anti-B7-H3 antibody-treated HCC murine model showed decreased tumor size and enhanced anti-tumor immunity mediated by CD8+ T cells. CONCLUSION: Altogether, our findings suggest that B7-H3 inhibition in tumor cells restores the immune cytotoxicity of T cells, which in turn promotes apoptosis of target cells. Therefore, B7-H3 serves as a key negative regulator in tumor immunity and the promising clinical utility of B7-H3-based immunotherapies for HCC treatment could be developed.

Relationship between certain hematological parameters and risk of breast cancer.

Aim: To explore the association between preoperative hemoglobin-to-red cell distribution width ratio (HRR), platelet-to-monocyte ratio or monocyte-to-high-density lipoprotein ratio and risk of breast cancer. Materials & methods: The clinical data of 226 patients with breast cancer were retrospectively analyzed and compared with 199 healthy controls by multivariate logistic regression analysis. Results: Multivariate logistic regression analysis revealed that HRR (p < 0.001) and monocyte-to-high-density lipoprotein ratio (p < 0.001) were independent predictors of breast cancer and lower HRR was associated with longer hospitalization, larger red cell distribution width value and lower hemoglobin level (p < 0.05). Conclusion: A significant association was found between HRR and clinical characteristics in breast cancer patients. Therefore, HRR is expected to become a novel and promising predictor of breast cancer.

Breast cancer is a common cancer, accounting for approximately 30% of all new cases of cancer diagnosed in women. It is also one of the main causes of cancer-related death in women. Clinically, breast cancer screening and early diagnosis rely mainly on mammography, ultrasound imaging, etc., but these tests are expensive and complex and are not suitable for early screening of breast cancer. This study found that low hemoglobin-to-red cell distribution width ratio and high monocyte-to-high-density lipoprotein ratio were associated with increased breast cancer risk. Because the determination of hemoglobin-to-red cell distribution width ratio and monocyte-to-high-density lipoprotein ratio is relatively simple, economic and convenient, regular detection of related markers can provide valuable information for early detection of breast cancer.

Comparative transcriptome analysis revealed molecular mechanisms of peanut leaves responding to Ralstonia solanacearum and its type III secretion system mutant.

Bacterial wilt caused by Ralstonia solanacearum is a serious soil-borne disease that limits peanut production and quality, but the molecular mechanisms of the peanut response to R. solanacearum remain unclear. In this study, we reported the first work analyzing the transcriptomic changes of the resistant and susceptible peanut leaves infected with R. solanacearum HA4-1 and its type III secretion system mutant strains by the cutting leaf method at different timepoints (0, 24, 36, and 72 h post inoculation). A total of 125,978 differentially expressed genes (DEGs) were identified and subsequently classified into six groups to analyze, including resistance-response genes, susceptibility-response genes, PAMPs induced resistance-response genes, PAMPs induced susceptibility-response genes, T3Es induced resistance-response genes, and T3Es induced susceptibility-response genes. KEGG enrichment analyses of these DEGs showed that plant-pathogen interaction, plant hormone signal transduction, and MAPK signaling pathway were the outstanding pathways. Further analysis revealed that CMLs/CDPKs-WRKY module, MEKK1-MKK2-MPK3 cascade, and auxin signaling played important roles in the peanut response to R. solanacearum. Upon R. solanacearum infection (RSI), three early molecular events were possibly induced in peanuts, including Ca2+ activating CMLs/CDPKs-WRKY module to regulate the expression of resistance/susceptibility-related genes, auxin signaling was induced by AUX/IAA-ARF module to activate auxin-responsive genes that contribute to susceptibility, and MEKK1-MKK2-MPK3-WRKYs was activated by phosphorylation to induce the expression of resistance/susceptibility-related genes. Our research provides new ideas and abundant data resources to elucidate the molecular mechanism of the peanut response to R. solanacearum and to further improve the bacterial wilt resistance of peanuts.

MiR-702-5p ameliorates diabetic encephalopathy in db/db mice by regulating 12/15-LOX.

The purpose of this study was to investigate the effect of miR-702-5p on diabetic encephalopathy (DE) and the interaction of miR-702-5p/12/15-LOX in the central nervous system (CNS). In this study, db/db mice were used as DE animal model and HT22 cells were treated with high-glucose (HG). Based on the bioinformatics prediction of possible binding sites between miR-702-5p and 12/15-LOX, we found that the expression of miR-702-5p was significantly down-regulated while 12/15-LOX up-regulated in vivo and in vitro, and the expression changes were inversely correlated. In vivo, diabetic mice with cognitive dysfunction and hippocampal neuronal damage had a concomitant increase in amyloid precursor protein (APP), amyloid beta(Aß), tau, BAX protein expressions; by contrast, Bcl-2 protein expression was significantly decreased. Overexpression of miR-702-5p significantly reduced the histopathological damage of the hippocampus, improved the learning and memory function of db/db mice, down-regulated 12/15-LOX, APP, Aß, tau, BAX protein expressions significantly and up-regulated the expression of Bcl-2. In vitro, miR-702-5p mimic reversed the decline in cell viability and the increase in cell apoptosis induced by HG. Simultaneously, reduced 12/15-LOX, APP, Aß, BAX protein expressions, and increased Bcl-2 protein expression were detected in the miR-702-5p mimic group. Moreover, combined administration of miR-702-5p mimic and 12/15-LOX overexpression lentivirus significantly reversed the protective effect of up-regulation of miR-702-5p. In conclusion, miR-702-5p has a neuroprotective effect on DE, and this effect was achieved by inhibiting 12/15-LOX. However, miR-702-5p had an endogenous regulatory effect on 12/15-LOX rather than a direct targeting relationship.

iPCD: A Comprehensive Data Resource of Regulatory Proteins in Programmed Cell Death.

Programmed cell death (PCD) is an essential biological process involved in many human pathologies. According to the continuous discovery of new PCD forms, a large number of proteins have been found to regulate PCD. Notably, post-translational modifications play critical roles in PCD process and the rapid advances in proteomics have facilitated the discovery of new PCD proteins. However, an integrative resource has yet to be established for maintaining these regulatory proteins. Here, we briefly summarize the mainstream PCD forms, as well as the current progress in the development of public databases to collect, curate and annotate PCD proteins. Further, we developed a comprehensive database, with integrated annotations for programmed cell death (iPCD), which contained 1,091,014 regulatory proteins involved in 30 PCD forms across 562 eukaryotic species. From the scientific literature, we manually collected 6493 experimentally identified PCD proteins, and an orthologous search was then conducted to computationally identify more potential PCD proteins. Additionally, we provided an in-depth annotation of PCD proteins in eight model organisms, by integrating the knowledge from 102 additional resources that covered 16 aspects, including post-translational modification, protein expression/proteomics, genetic variation and mutation, functional annotation, structural annotation, physicochemical property, functional domain, disease-associated information, protein-protein interaction, drug-target relation, orthologous information, biological pathway, transcriptional regulator, mRNA expression, subcellular localization and DNA and RNA element. With a data volume of 125 GB, we anticipate that iPCD can serve as a highly useful resource for further analysis of PCD in eukaryotes.

Maternal Prenatal Inflammation Increases Brain Damage Susceptibility of Lipopolysaccharide in Adult Rat Offspring via COX-2/PGD-2/DPs Pathway Activation.

A growing body of research suggests that inflammatory insult contributes to the etiology of central nervous system diseases, such as depression, Alzheimer's disease, and so forth. However, the effect of prenatal systemic inflammation exposure on offspring brain development and cerebral susceptibility to inflammatory insult remains unknown. In this study, we utilized the prenatal inflammatory insult model in vivo and the neuronal damage model in vitro. The results obtained show that prenatal maternal inflammation exacerbates LPS-induced memory impairment, neuronal necrosis, brain inflammatory response, and significantly increases protein expressions of COX-2, DP2, APP, and Aß, while obviously decreasing that of DP1 and the exploratory behaviors of offspring rats. Meloxicam significantly inhibited memory impairment, neuronal necrosis, oxidative stress, and inflammatory response, and down-regulated the expressions of APP, Aß, COX-2, and DP2, whereas significantly increased exploring behaviors and the expression of DP1 in vivo. Collectively, these findings suggested that maternal inflammation could cause offspring suffering from inflammatory and behavioral disorders and increase the susceptibility of offspring to cerebral pathological factors, accompanied by COX-2/PGD-2/DPs pathway activation, which could be ameliorated significantly by COX-2 inhibitor meloxicam treatment.

Maternal Inflammation Exaggerates Offspring Susceptibility to Cerebral Ischemia-Reperfusion Injury via the COX-2/PGD2/DP2 Pathway Activation.

The pathogenesis of cerebral ischemia-reperfusion (I/R) injury is complex and does not exhibit an effective strategy. Maternal inflammation represents one of the most important factors involved in the etiology of brain injury in newborns. We aimed to investigate the effect of maternal inflammation on offspring susceptibility to cerebral I/R injury and the mechanisms by which it exerts its effects. Pregnant SD rats were intraperitoneally injected with LPS (300 µg/kg/day) at gestational days 11, 14, and 18. Pups were subjected to MCAO/R on postnatal day 60. Primary neurons were obtained from postnatal day 0 SD rats and subjected to OGD/R. Neurological deficits, brain injury, neuronal viability, neuronal damage, and neuronal apoptosis were assessed. Oxidative stress and inflammation were evaluated, and the expression levels of COX-2/PGD2/DP pathway-related proteins and apoptotic proteins were detected. Maternal LPS exposure significantly increased the levels of oxidative stress and inflammation, significantly activated the COX-2/PGD2/DP2 pathway, and increased proapoptotic protein expression. However, maternal LPS exposure significantly decreased the antiapoptotic protein expression, which subsequently increased neurological deficits and cerebral I/R injury in offspring rats. The corresponding results were observed in primary neurons. Moreover, these effects of maternal LPS exposure were reversed by a COX-2 inhibitor and DP1 agonist but exacerbated by a DP2 agonist. In conclusion, maternal inflammatory exposure may increase offspring susceptibility to cerebral I/R injury. Moreover, the underlying mechanism might be related to the activation of the COX-2/PGD2/DP2 pathway. These findings provide a theoretical foundation for the development of therapeutic drugs for cerebral I/R injury.

Complete Genome Sequence Analysis of Ralstonia solanacearum Strain PeaFJ1 Provides Insights Into Its Strong Virulence in Peanut Plants.

The bacterial wilt of peanut (Arachis hypogaea L.) caused by Ralstonia solanacearum is a devastating soil-borne disease that seriously restricted the world peanut production. However, the molecular mechanism of R. solanacearum-peanut interaction remains largely unknown. We found that R. solanacearum HA4-1 and PeaFJ1 isolated from peanut plants showed different pathogenicity by inoculating more than 110 cultivated peanuts. Phylogenetic tree analysis demonstrated that HA4-1 and PeaFJ1 both belonged to phylotype I and sequevar 14M, which indicates a high degree of genomic homology between them. Genomic sequencing and comparative genomic analysis of PeaFJ1 revealed 153 strain-specific genes compared with HA4-1. The PeaFJ1 strain-specific genes consisted of diverse virulence-related genes including LysR-type transcriptional regulators, two-component system-related genes, and genes contributing to motility and adhesion. In addition, the repertoire of the type III effectors of PeaFJ1 was bioinformatically compared with that of HA4-1 to find the candidate effectors responsible for their different virulences. There are 79 effectors in the PeaFJ1 genome, only 4 of which are different effectors compared with HA4-1, including RipS4, RipBB, RipBS, and RS_T3E_Hyp6. Based on the virulence profiles of the two strains against peanuts, we speculated that RipS4 and RipBB are candidate virulence effectors in PeaFJ1 while RipBS and RS_T3E_Hyp6 are avirulence effectors in HA4-1. In general, our research greatly reduced the scope of virulence-related genes and made it easier to find out the candidates that caused the difference in pathogenicity between the two strains. These results will help to reveal the molecular mechanism of peanut-R. solanacearum interaction and develop targeted control strategies in the future.

miR-204-5p is sponged by TUG1 to aggravate neuron damage induced by focal cerebral ischemia and reperfusion injury through upregulating COX2.

Studies have reported that miR-204-5p is involved in multiple biological processes. However, little is known about the expression and mechanism of miR-204-5p in cerebral ischemia and reperfusion injury. This study found that miR-204-5p expression was significantly downregulated in the blood of patients with ischemic stroke, MCAO/R rat brains, and OGD/R neurons. Overexpression of miR-204-5p markedly reduced infarct volume and neurological impairment and alleviated the inflammatory response in vivo. miR-204-5p promoted neuronal viability and reduced apoptotic cells in vitro. Mechanically, miR-204-5p was negatively regulated by the expression lncRNA TUG1 upstream and down-regulated COX2 expression downstream. Therefore, the TUG1/miR-204-5p/COX2 axis was involved in ischemia and reperfusion-induced neuronal damage. This finding may provide a novel strategy for the treatment of cerebral ischemia and reperfusion injury.

Discovery of Novel and Highly Potent Inhibitors of SARS CoV-2 Papain-Like Protease Through Structure-Based Pharmacophore Modeling, Virtual Screening, Molecular Docking, Molecular Dynamics Simulations, and Biological Evaluation.

Background and Objective: COVID-19 has struck our society as a great calamity, and the need for effective anti-viral drugs is more urgent than ever. Papain-like protease (PLpro) of SARS CoV-2 plays important roles in virus maturation, dysregulation of host inflammation, and antiviral immune responses, which is being regarded as a promising druggable target for the treatment of COVID-19. Here, we carried out a combined screening approach to identify novel and highly potent PLpro inhibitors for the treatment of COVID-19. Methods: We used a combined screening approach of structure-based pharmacophore modeling and molecular docking to screen an in-house database containing 35,000 compounds. SARS CoV-2 PLpro inhibition assay was used to carry out the biological evaluation of hit compounds. Molecular dynamics (MD) simulations were conducted to check the stability of the PLpro-hit complexes predicted by molecular docking. Results: We found that four hit compounds showed excellent inhibitory activities against PLpro with IC50 values ranging from 0.6 to 2.4 µM. Among them, the most promising compound, hit 2 is the best PLpro inhibitor and its inhibitory activity was about 4 times higher than that of the positive control (GRL0617). The study of MD simulations indicated that four hits could bind stably to the active site of PLpro. Further study of interaction analysis indicated that hit 2 could form hydrogen-bond interactions with the key amino acids such as Gln269 and Asp164 in the PLpro-active site. Conclusion: Hit 2 is a novel and highly potent PLpro inhibitor, which will open the way for the development of clinical PLpro inhibitors for the treatment of COVID-19.

GPS-Uber: a hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites.

As an important post-translational modification, lysine ubiquitination participates in numerous biological processes and is involved in human diseases, whereas the site specificity of ubiquitination is mainly decided by ubiquitin-protein ligases (E3s). Although numerous ubiquitination predictors have been developed, computational prediction of E3-specific ubiquitination sites is still a great challenge. Here, we carefully reviewed the existing tools for the prediction of general ubiquitination sites. Also, we developed a tool named GPS-Uber for the prediction of general and E3-specific ubiquitination sites. From the literature, we manually collected 1311 experimentally identified site-specific E3-substrate relations, which were classified into different clusters based on corresponding E3s at different levels. To predict general ubiquitination sites, we integrated 10 types of sequence and structure features, as well as three types of algorithms including penalized logistic regression, deep neural network and convolutional neural network. Compared with other existing tools, the general model in GPS-Uber exhibited a highly competitive accuracy, with an area under curve values of 0.7649. Then, transfer learning was adopted for each E3 cluster to construct E3-specific models, and in total 112 individual E3-specific predictors were implemented. Using GPS-Uber, we conducted a systematic prediction of human cancer-associated ubiquitination events, which could be helpful for further experimental consideration. GPS-Uber will be regularly updated, and its online service is free for academic research at http://gpsuber.biocuckoo.cn/.

CPLM 4.0: an updated database with rich annotations for protein lysine modifications.

Here, we reported the compendium of protein lysine modifications (CPLM 4.0, http://cplm.biocuckoo.cn/), a data resource for various post-translational modifications (PTMs) specifically occurred at the side-chain amino group of lysine residues in proteins. From the literature and public databases, we collected 450 378 protein lysine modification (PLM) events, and combined them with the existing data of our previously developed protein lysine modification database (PLMD 3.0). In total, CPLM 4.0 contained 592 606 experimentally identified modification events on 463 156 unique lysine residues of 105 673 proteins for up to 29 types of PLMs across 219 species. Furthermore, we carefully annotated the data using the knowledge from 102 additional resources that covered 13 aspects, including variation and mutation, disease-associated information, protein-protein interaction, protein functional annotation, DNA & RNA element, protein structure, chemical-target relation, mRNA expression, protein expression/proteomics, subcellular localization, biological pathway annotation, functional domain annotation, and physicochemical property. Compared to PLMD 3.0 and other existing resources, CPLM 4.0 achieved a >2-fold increase in collection of PLM events, with a data volume of ∼45GB. We anticipate that CPLM 4.0 can serve as a more useful database for further study of PLMs.