Gut microbiota mediates anxiety-like behaviors induced by chronic infection of Toxoplasma gondii in mice.

BACKGROUND: Chronic infection with the neurotropic parasite Toxoplasma gondii (T. gondii) can cause anxiety and gut microbiota dysbiosis in hosts. However, the potential role of gut microbiota in anxiety induced by the parasite remains unclear. METHODS: C57BL/6J mice were infected with 10 cysts of T. gondii. Antibiotic depletion of gut microbiota and fecal microbiota transplantation experiments were utilized to investigate the causal relationship between gut microbiota and anxiety. Anxiety-like behaviors were examined by the elevated plus maze test and the open field test; blood, feces, colon and amygdala were collected to evaluate the profiles of serum endotoxin (Lipopolysaccharide, LPS) and serotonin (5-hydroxytryptamine, 5-HT), gut microbiota composition, metabolomics, global transcriptome and neuroinflammation in the amygdala. Furthermore, the effects of Diethyl butylmalonate (DBM, an inhibitor of mitochondrial succinate transporter, which causes the accumulation of endogenous succinate) on the disorders of the gut-brain axis were evaluated. RESULTS: Here, we found that T. gondii chronic infection induced anxiety-like behaviors and disturbed the composition of the gut microbiota in mice. In the amygdala, T. gondii infection triggered the microglial activation and neuroinflammation. In the colon, T. gondii infection caused the intestinal dyshomeostasis including elevated colonic inflammation, enhanced bacterial endotoxin translocation to blood and compromised intestinal barrier. In the serum, T. gondii infection increased the LPS levels and decreased the 5-HT levels. Interestingly, antibiotics ablation of gut microbiota alleviated the anxiety-like behaviors induced by T. gondii infection. More importantly, transplantation of the fecal microbiota from T. gondii-infected mice resulted in anxiety and the transcriptomic alteration in the amygdala of the antibiotic-pretreated mice. Notably, the decreased abundance of succinate-producing bacteria and the decreased production of succinate were observed in the feces of the T. gondii-infected mice. Moreover, DBM administration ameliorated the anxiety and gut barrier impairment induced by T. gondii infection. CONCLUSIONS: The present study uncovers a novel role of gut microbiota in mediating the anxiety-like behaviors induced by chronic T. gondii infection. Moreover, we show that DBM supplementation has a beneficial effect on anxiety. Overall, these findings provide new insights into the treatment of T. gondii-related mental disorders.

Effect of HDAC9 on the differentiation of chicken embryonic stem cells into male germ cells.

Histone deacetylase 9 (HDAC9) is a histone deacetylase (HDAC) subtype IIa protein that deacetylates histone 3 (H3), histone 4 (H4), and nonhistone proteins in vivo to alter chromosomal shape and regulate gene transcription. There have been few studies on the regulatory influence of the HDAC9 gene on the differentiation of chicken embryonic stem cells (cESCs) into male germ cells, and the significance of HDAC9 is still unknown. Therefore, we explored the specific role of HDAC9 during differentiation of the cESCs of Jilin Luhua chickens through inhibition or overexpression. In medium supplemented with 10-5 mol/L retinoic acid (RA), cESCs were stimulated to develop into germ cells. HDAC9 and germline marker gene mRNA and protein levels were measured using qRT‒PCR and western blotting. During the differentiation of cESCs into male germ cells, overexpression of the HDAC9 gene greatly increased the mRNA and protein expression levels of the germline marker genes Stra8, Dazl, c-kit, and integrin ɑ6. The HDAC9 inhibitor TMP195 significantly decreased the mRNA and protein expression levels of the above markers. In summary, HDAC9 positively regulates the differentiation of cESCs.

Follicular fluid exosome-derived miR-339-5p enhances in vitro maturation of porcine oocytes via targeting SFPQ, a regulator of the ERK1/2 pathway.

In this study, we aimed to investigate cytoplasmic maturation and miRNA expression of mature oocytes cultured in porcine follicular fluid exosomes. We also examined the effect of miR-339-5p on oocyte maturation. Twenty eight differentially expressed miRNAs were detected using miRNA-seq. We then transfected cumulus oocyte complexes with miR-339-5p mimics and inhibitor during culture. The results showed that exosomes increased endoplasmic reticulum levels and the amount of lipid droplets, and decreased ROS levels, lipid droplet size, and percentage of oocytes with abnormal cortical granule distribution. Overexpressing miR-339-5p significantly decreased cumulus expansion genes, oocyte maturation-related genes, target gene proline/glutamine-rich splicing factor (SFPQ), ERK1/2 phosphorylation levels, oocyte maturation rate, blastocyst rate, and lipid droplet number, but increased lipid droplet size and the ratio of oocytes with abnormal cortical granule distribution. Inhibiting miR-339-5p reversed the decrease observed during overexpression. Mitochondrial membrane potential and ROS levels did not differ significantly between groups. In summary, exosomes promote oocyte cytoplasmic maturation and miR-339-5p regulating ERK1/2 activity through SFPQ expression, thereby elevating oocyte maturation and blastocyst formation rate in vitro.

TSCRE: a comprehensive database for tumor-specific cis-regulatory elements.

Cis-regulatory elements (CREs) and super cis-regulatory elements (SCREs) are non-coding DNA regions which influence the transcription of nearby genes and play critical roles in development. Dysregulated CRE and SCRE activities have been reported to alter the expression of oncogenes and tumor suppressors, thereby regulating cancer hallmarks. To address the strong need for a comprehensive catalogue of dysregulated CREs and SCREs in human cancers, we present TSCRE (http://tscre.zsqylab.com/), an open resource providing tumor-specific and cell type-specific CREs and SCREs derived from the re-analysis of publicly available histone modification profiles. Currently, TSCRE contains 1 864 941 dysregulated CREs and 68 253 dysregulated SCREs identified from 1366 human patient samples spanning 17 different cancer types and 9 histone marks. Over 95% of these elements have been validated in public resources. TSCRE offers comprehensive annotations for each element, including associated genes, expression patterns, clinical prognosis, somatic mutations, transcript factor binding sites, cancer-type specificity, and drug response. Additionally, TSCRE integrates pathway and transcript factor enrichment analyses for each study, enabling in-depth functional and mechanistic investigations. Furthermore, TSCRE provides an interactive interface for users to explore any CRE and SCRE of interest. We believe TSCRE will be a highly valuable platform for the community to discover candidate cancer biomarkers.

BioTreasury: a community-based repository enabling indexing and rating of bioinformatics tools.

The exponential growth of bioinformatics tools in recent years has posed challenges for scientists in selecting the most suitable one for their data analysis assignments. Therefore, to aid scientists in making informed choices, a community-based platform that indexes and rates bioinformatics tools is urgently needed. In this study, we introduce BioTreasury ( http://biotreasury.rjmart.cn ), an integrated community-based repository that provides an interactive platform for users and developers to share their experiences in various bioinformatics tools. BioTreasury offers a comprehensive collection of well-indexed bioinformatics software, tools, and databases, totaling over 10,000 entries. In the past two years, we have continuously improved and maintained BioTreasury, adding several exciting features, including creating structured homepages for every tool and user, a hierarchical category of bioinformatics tools and classifying tools using large language model (LLM). BioTreasury streamlines the tool submission process with intelligent auto-completion. Additionally, BioTreasury provides a wide range of social features, for example, enabling users to participate in interactive discussions, rate tools, build and share tool collections for the public. We believe BioTreasury can be a valuable resource and knowledge-sharing platform for the biomedical community. It empowers researchers to effectively discover and evaluate bioinformatics tools, fostering collaboration and advancing bioinformatics research.

ß-Glucan alleviates goal-directed behavioral deficits in mice infected with Toxoplasma gondii.

BACKGROUND: Toxoplasma gondii (T. gondii) is a neuroinvasive parasite causing neuroinflammation, which in turn is associated with a higher risk for several psycho-behavioral disorders. There is an urgent need to identify drugs capable of improving cognitive deficits induced by T. gondii infection. ß-Glucan, an active ingredient in mushrooms, could significantly enhance immunity. However, the effects of ß-glucan against neuroinflammation and cognitive decline induced by T. gondii infection remain unknown. The present study aimed to investigate the neuroprotective effect of ß-glucan on goal-directed behavior of mice chronically infected by T. gondii Wh6 strain. METHODS: A mice model of chronic T. gondii Wh6 infection was established by infecting mice by oral gavage with 10 cysts of T. gondii Wh6. Intraperitoneal injection of ß-glucan was manipulated 2 weeks before T. gondii infection. Performance of the infected mice on the Y-maze test and temporal order memory (TOM) test was used to assess the goal-directed behavior. Golgi-Cox staining, transmission electron microscopy, immunofluorescence, real-time PCR and western blot assays were used to detect prefrontal cortex-associated pathological change and neuroinflammation. RESULTS: The administration of ß-glucan significantly prevented T. gondii Wh6-induced goal-directed behavioral impairment as assessed behaviorally by the Y-maze test and TOM test. In the prefrontal cortex, ß-glucan was able to counter T. gondii Wh6-induced degeneration of neurites, impairment of synaptic ultrastructure and decrease of pre- and postsynaptic protein levels. Also, ß-glucan significantly prevented the hyperactivation of pro-inflammatory microglia and astrocytes, as well as the upregulation of proinflammatory cytokines caused by chronic T. gondii Wh6 infection. CONCLUSIONS: This study revealed that ß-glucan prevents goal-directed behavioral impairment induced by chronic T. gondii infection in mice. These findings suggest that ß-glucan may be an effective drug candidate to prevent T. gondii-associated psycho-behavioral disorders including goal-directed behavioral injury.

Lattice Network for Lightweight Image Restoration.

Deep learning has made unprecedented progress in image restoration (IR), where residual block (RB) is popularly used and has a significant effect on promising performance. However, the massive stacked RBs bring about burdensome memory and computation cost. To tackle this issue, we aim to design an economical structure for adaptively connecting pair-wise RBs, thereby enhancing the model representation. Inspired by the topological structure of lattice filter in signal processing theory, we elaborately propose the lattice block (LB), where couple butterfly-style topological structures are utilized to bridge pair-wise RBs. Specifically, each candidate structure of LB relies on the combination coefficients learned through adaptive channel reweighting. As a basic mapping block, LB can be plugged into various IR models, such as image super-resolution, image denoising, image deraining, etc. It can avail the construction of lightweight IR models accompanying half parameter amount reduced, while keeping the considerable reconstruction accuracy compared with RBs. Moreover, a novel contrastive loss is exploited as a regularization constraint, which can further enhance the model representation without increasing the inference expenses. Experiments on several IR tasks illustrate that our method can achieve more favorable performance than other state-of-the-art models with lower storage and computation.

RM2Target: a comprehensive database for targets of writers, erasers and readers of RNA modifications.

RNA modification is a dynamic and reversible process regulated by a series of writers, erasers and readers (WERs). Abnormal changes of WERs will disrupt the RNA modification homeostasis of their target genes, leading to the dysregulation of RNA metabolisms such as RNA stability and translation, and consequently to diseases such as cancer. A public repository hosting the regulatory relationships between WERs and their target genes will help in understanding the roles of RNA modifications in various physiological and pathological conditions. Previously, we developed a database named 'm6A2Target' to host targets of WERs in m6A, one of the most prevalent RNA modifications in eukaryotic cells. To host all RNA modification (RM)-related WER-target associations, we hereby present an updated database, named 'RM2Target' (http://rm2target.canceromics.org/). In this update, RM2Target encompasses 1 619 653 WER-target associations for nine RNA modifications in human and mouse, including m6A, m6Am, m5C, m5U, m1A, m7G, pseudouridine, 2'-O-Me and A-to-I. Extensive annotations of target genes are available in RM2Target, including but not limited to basic gene information, RNA modifications, RNA-RNA/RNA-protein interactions and related diseases. Altogether, we expect that RM2Target will facilitate further downstream functional and mechanistic studies in the field of RNA modification research.

Analysis of microRNA expression profiles during the differentiation of chicken embryonic stem cells into male germ cells.

The differentiation of embryonic stem cells (ESCs) into germ cells in vitro could have very promising applications for infertility treatment and could provide an excellent model for uncovering the molecular mechanisms of germline generation. This study aimed to investigate the differentially expressed miRNAs (DEMs) during the differentiation of chicken ESCs (cESCs) into male germ cells and to establish a profile of the DEMs. Cells before and after induction were subjected to miRNA sequencing (miRNA-seq). A total of 113 DEMs were obtained, including 61 upregulated and 52 downregulated DEMs. GO and KEGG enrichment analyses showed that the target genes were enriched mainly in the MAPK signaling pathway, HTLV infection signaling pathway, cell adhesion molecule (CAM)-related pathways, viral myocarditis, Wnt signaling pathway, ABC transporters, TGF-ß signaling pathways, Notch signaling pathways and insulin signaling pathway. The target genes of the miRNAs were related to cell binding, cell parts and biological regulatory processes. Six DEMs, let-7k-5p, miR-132c-5p, miR-193a-5p, miR-202-5p, miR-383-5p and miR-6553-3p, were assessed by qRT-PCR, and the results were consistent with the results of miRNA-seq. Based on qRT-PCR and western blot verification, miR-383-5p and its putative target gene STRN3 were selected to construct an STRN3 3'-UTR dual-luciferase gene reporter vector and its mutant vector. The double luciferase reporter activity of the cotransfected STRN3-WT + miR-383-5p mimics group was significantly lower (by approximately 46%) than that of the other five groups (p < 0.01). There was no significant difference in luciferase activity among the other 5 groups. This study establishes a DEM profile during the process of cESC differentiation into male germ cells; illustrates the mechanisms by which miRNAs regulate target genes; provides a theoretical basis for further research on the mechanisms of the formation and regulation of male germ cells; and provides an important strategy for gene editing, animal genetic resource protection and transgenic animal production.

Rottlerin plays an antiviral role at early and late steps of Zika virus infection.

Infection of Zika virus (ZIKV) may cause microcephaly and other neurological disorders, while no vaccines and drugs are available. Our study revealed that rottlerin confers a broad antiviral activity against several enveloped viruses, including ZIKV, vesicular stomatitis virus, and herpes simplex virus, but not against two naked viruses (enterovirus 71 and encephalomyocarditis virus). Rottlerin does not have a direct virucidal effect on the virions, and its antiviral effect is independent of its regulation on PKCδ or ATP. Both pretreatment and post-treatment of rottlerin effectively reduce the viral replication of ZIKV. The pretreatment of rottlerin disturbs the endocytosis of enveloped viruses, while the post-treatment of rottlerin acts at a late stage through disturbing the maturation of ZIKV. Importantly, administration of rottlerin in neonatal mice significantly decreased the ZIKV replication in vivo, and alleviated the neurological symptoms caused by ZIKV. Our work suggests that rottlerin exerts an antiviral activity at two distinct steps of viral infection, and can be potentially developed as a prophylactic and therapeutic agent.

Heat-shock protein 90α is a potential prognostic and predictive biomarker in hepatocellular carcinoma: a large-scale and multicenter study.

BACKGROUND: Although the diagnostic value of plasma heat-shock protein 90α (HSP90α) in hepatocellular carcinoma (HCC) has been previously reported, the causal effect of the plasma HSP90α levels on HCC prognosis remains largely unclear. To this extent, we sought to assess whether the plasma HSP90α acts as a prognostic factor for HCC patients. METHODS: A total of 2150 HCC patients were included in this retrospective study between August 2016 and July 2021. Plasma HSP90α levels were tested within a week before treatment and their association with prognosis was assessed. RESULTS: An optimal cutoff value of 143.5 for the HSP90α based on the overall survival (OS) was determined using the X-tile software. HCC patients with HSP90α < 143.5 ng/mL (low HSP90α) before and after propensity score matching (PSM) indicated longer median OS (mOS) relative to those with HSP90α ≥ 143.5 ng/mL (high HSP90α) (37.0 vs. 9.0 months, p < 0.001; 19.2 vs. 9.6 months, p < 0.001; respectively). In addition, the high HSP90α plasma level is an independent poor prognostic factor for OS in HCC patients. In our subgroup analysis, including the supportive care group, surgery group, transarterial chemoembolization (TACE) group, adjuvant TACE group, an immune checkpoint inhibitor (ICI) plus targeted therapy group, and TACE plus ICI group, the high HSP90α group demonstrated better OS compared to the low HSP90α group. Moreover, in the supportive care, TACE, ICI plus targeted therapy, TACE plus ICI groups, and high HSP90α levels were also an independent poor prognostic factors for OS. CONCLUSIONS: Our study confirmed that the plasma HSP90α level can be used as a prognostic biomarker for HCC.

Gamma knife radiosurgery versus transcatheter arterial chemoembolization for hepatocellular carcinoma with portal vein tumor thrombus: a propensity score matching study.

BACKGROUND: The optimal locoregional treatment for hepatocellular carcinoma (HCC) patients with portal vein tumor thrombus (PVTT) is unclear. This study aimed to investigate the efficacy of Gamma knife radiosurgery (GKR) versus transcatheter arterial chemoembolization (TACE) in HCC patients with PVTT. METHODS: This retrospective study included 544 HCC patients with PVTT (GKR, 202; TACE, 342). Propensity score matching (PSM) analysis identified 171 matched pairs of patients. The primary endpoint was overall survival (OS). RESULTS: Before PSM, the GKR group exhibited longer median OS (mOS) than the TACE group (17.2 vs. 8.0 months, p < 0.001). We followed the Cheng's classification for PVTT. In the subgroup analysis, GKR was associated with significantly longer mOS for patients with PVTT II-IV (17.5 vs. 8.7 months, p < 0.001; 17.2 vs. 7.8 months, p = 0.001; 14.5 vs. 6.5 months, p = 0.001, respectively) and comparable OS for patients with PVTT I. After PSM, the GKR group had also a longer mOS than the TACE group (15.8 vs. 10.4 months, p < 0.001). In the subgroup analysis, the GKR group demonstrated superior mOS for patients with PVTT II-IV (all p < 0.05) and comparable OS for patients with PVTT I. CONCLUSIONS: GKR was associated better OS than TACE in HCC patients with PVTT, especially for patients with PVTT II-IV. CLINICAL TRIALS REGISTRATION: The study was registered in the Chinese Clinical Trials Registry under the registration number ChiCTR2100051057.

IBS 2.0: an upgraded illustrator for the visualization of biological sequences.

The visualization of biological sequences with various functional elements is fundamental for the publication of scientific achievements in the field of molecular and cellular biology. However, due to the limitations of the currently used applications, there are still considerable challenges in the preparation of biological schematic diagrams. Here, we present a professional tool called IBS 2.0 for illustrating the organization of both protein and nucleotide sequences. With the abundant graphical elements provided in IBS 2.0, biological sequences can be easily represented in a concise and clear way. Moreover, we implemented a database visualization module in IBS 2.0, enabling batch visualization of biological sequences from the UniProt and the NCBI RefSeq databases. Furthermore, to increase the design efficiency, a resource platform that allows uploading, retrieval, and browsing of existing biological sequence diagrams has been integrated into IBS 2.0. In addition, a lightweight JS library was developed in IBS 2.0 to assist the visualization of biological sequences in customized web services. To obtain the latest version of IBS 2.0, please visit https://ibs.renlab.org.

MicroRNA-101 regulates oocyte maturation in vitro via targeting HAS2 in porcine cumulus cells.

RNA-seq technology can be used for the detection of miRNA transcripts in tissues and cells at specific periods and under specific treatment conditions, which can easily and effectively screen out differential transcripts. The purpose of this study was to compare miRNA expression in porcine cumulus cells before and after oocyte maturation, and to investigate the mechanism whereby cumulus cells may influence oocyte maturation. To that aim, cumulus cells surrounding GV- and MII-stage oocytes were isolated, and their differences in miRNA expression were examined using miRNA-seq. 143 differentially expressed miRNAs were identified, among which miR-101 was selected and further verified by qPCR. Moreover, miR-101 was found to target HAS2 through target gene prediction, luciferase-based co-transfection and cumulus cells transfection. Transfection of COCs with miR-101 mimics or inhibitor revealed that the miR-101 could inhibit oocyte IVM by regulating the expanding of CCSs, but had no effect on the embryo development competence. These findings demonstrated that miR-101 regulated oocyte maturation in vitro via targeting HAS2 in porcine cumulus cells.

Effects of partially replacing glycerol with cholesterol-loaded cyclodextrin on protamine deficiency, in vitro capacitation and fertilization ability of frozen-thawed Yanbian Yellow cattle sperm.

Glycerol is widely used as a cryoprotectant to protect the sperm from freezing damage during cryopreservation. However, glycerol at a high concentration has toxic effects on the sperm. Therefore, we explored the effects of partially replacing glycerol with cholesterol-loaded cyclodextrin (CLC) in a cryoprotectant on protamine deficiency, in vitro capacitation, and fertilization ability of freeze-thawed Yanbian Yellow cattle sperm. We used fresh semen, control (6% glycerol), and four treatment-I, II, III, and IV (3% glycerol + 0, 0.75, 1.5, and 3 mg/mL CLC, respectively)-groups. Computer-assisted semen analysis; JC-1, CMA3, and FluoZin-3-AM staining; flow cytometry; and IVF were conducted. Replacing a portion of glycerol with 1.5 mg/mL CLC significantly improved sperm motility, viability, plasma membrane integrity, acrosome integrity, and membrane lipid disorders, mitochondrial membrane potential (MMP), capacitation, and fertilization ability (P < 0.05) compared with the control. Additionally, in group I and III, the protamine deficiency were significantly lower (P < 0.05) than in the control group. It was found that 6% glycerol has a higher degree of damage to sperm DNA integrity than 3% glycerol. Overall, this study revealed that partial replacement of glycerol with CLC can be used as a novel cryoprotection method to reduce the toxicity of glycerol and improve the quality of thawed Yanbian Yellow cattle sperm.

SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients.

As an increasing number of noncoding RNAs (ncRNAs) have been suggested to encode short bioactive peptides in cancer, the exploration of ncRNA-encoded small peptides (ncPEPs) is emerging as a fascinating field in cancer research. To assist in studies on the regulatory mechanisms of ncPEPs, we describe here a database called SPENCER (http://spencer.renlab.org). Currently, SPENCER has collected a total of 2806 mass spectrometry (MS) data points from 55 studies, covering 1007 tumor samples and 719 normal samples. Using an MS-based proteomics analysis pipeline, SPENCER identified 29 526 ncPEPs across 15 different cancer types. Specifically, 22 060 of these ncPEPs were experimentally validated in other studies. By comparing tumor and normal samples, the identified ncPEPs were divided into four expression groups: tumor-specific, upregulated in cancer, downregulated in cancer, and others. Additionally, since ncPEPs are potential targets for neoantigen-based cancer immunotherapy, SPENCER also predicted the immunogenicity of all the identified ncPEPs by assessing their MHC-I binding affinity, stability, and TCR recognition probability. As a result, 4497 ncPEPs curated in SPENCER were predicted to be immunogenic. Overall, SPENCER will be a useful resource for investigating cancer-associated ncPEPs and may boost further research in cancer.

RPS: a comprehensive database of RNAs involved in liquid-liquid phase separation.

Liquid-liquid phase separation (LLPS) is critical for assembling membraneless organelles (MLOs) such as nucleoli, P-bodies, and stress granules, which are involved in various physiological processes and pathological conditions. While the critical role of RNA in the formation and the maintenance of MLOs is increasingly appreciated, there is still a lack of specific resources for LLPS-related RNAs. Here, we presented RPS (http://rps.renlab.org), a comprehensive database of LLPS-related RNAs in 20 distinct biomolecular condensates from eukaryotes and viruses. Currently, RPS contains 21,613 LLPS-related RNAs with three different evidence types, including 'Reviewed', 'High-throughput' and 'Predicted'. RPS provides extensive annotations of LLPS-associated RNA properties, including sequence features, RNA structures, RNA-protein/RNA-RNA interactions, and RNA modifications. Moreover, RPS also provides comprehensive disease annotations to help users to explore the relationship between LLPS and disease. The user-friendly web interface of RPS allows users to access the data efficiently. In summary, we believe that RPS will serve as a valuable platform to study the role of RNA in LLPS and further improve our understanding of the biological functions of LLPS.

DeepOMe: A Web Server for the Prediction of 2'-O-Me Sites Based on the Hybrid CNN and BLSTM Architecture.

2'-O-methylations (2'-O-Me or Nm) are one of the most important layers of regulatory control over gene expression. With increasing attentions focused on the characteristics, mechanisms and influences of 2'-O-Me, a revolutionary technique termed Nm-seq were established, allowing the identification of precise 2'-O-Me sites in RNA sequences with high sensitivity. However, as the costs and complexities involved with this new method, the large-scale detection and in-depth study of 2'-O-Me is still largely limited. Therefore, the development of a novel computational method to identify 2'-O-Me sites with adequate reliability is urgently needed at the current stage. To address the above issue, we proposed a hybrid deep-learning algorithm named DeepOMe that combined Convolutional Neural Networks (CNN) and Bidirectional Long Short-term Memory (BLSTM) to accurately predict 2'-O-Me sites in human transcriptome. Validating under 4-, 6-, 8-, and 10-fold cross-validation, we confirmed that our proposed model achieved a high performance (AUC close to 0.998 and AUPR close to 0.880). When testing in the independent data set, DeepOMe was substantially superior to NmSEER V2.0. To facilitate the usage of DeepOMe, a user-friendly web-server was constructed, which can be freely accessed at http://deepome.renlab.org.

Characterization of DinJ-YafQ toxin-antitoxin module in Tetragenococcus halophilus: activity, interplay, and evolution.

Tetragenococcus halophilus is a moderately halophilic lactic acid bacterium widely used in high-salt food fermentation because of its coping ability under various stress conditions. Bacterial toxin-antitoxin (TA) modules are widely distributed and play important roles in stress response, but those specific for genus Tetragenococcus have never been explored. Here, a bona fide TA module named DinJ1-YafQ1tha was characterized in T. halophilus. The toxin protein YafQ1tha acts as a ribonuclease, and its overexpression severely inhibits Escherichia coli growth. These toxic effects can be eliminated by introducing DinJ1tha, indicating that YafQ1tha activity is blocked by the formed DinJ1-YafQ1tha complex. In vivo and in vitro assays showed that DinJ1tha alone or DinJ1-YafQ1tha complex can repress the transcription of dinJ1-yafQ1tha operon by binding directly to the promoter sequence. In addition, dinJ1-yafQ1tha is involved in plasmid maintenance and stress response, and its transcriptional level is regulated by various stresses. These findings reveal the possible roles of DinJ1-YafQ1tha system in the stress adaptation processes of T. halophilus during fermentation. A single antitoxin DinJ2tha without a cognate toxin protein was also found. Its sequence shows low similarity to that of DinJ1tha, indicating that this antitoxin may have evolved from a different ancestor. Moreover, DinJ2tha can cross-interact with noncognate toxin YafQ1tha and cross-regulate with dinJ1-yafQ1tha operon. In summary, DinJ-YafQtha characterization may be helpful in investigating the key roles of TA systems in T. halophilus and serves as a foundation for further research. KEY POINTS: • dinJ1-yafQ1tha is the first functional TA module characterized in T. halophilus and upregulated significantly upon osmotic and acidic stress. • DinJ2tha can exhibit physical and transcriptional interplay with DinJ1-YafQ1tha. • dinJ2tha may be acquired from bacteria in distant affiliation and inserted into the T. halophilus genome through horizontal gene transfer.

Effects of the E1 activating enzyme UBA2 on porcine oocyte maturation, apoptosis, and embryonic development in vitro.

The purpose of this study was to investigate the effect of the E1 activating enzyme UBA2 on the expression of the SUMO-1 protein during in vitro maturation (IVM) of pig oocytes and embryonic development. In the 5 µg/ml UBA2 treatment group, the expression of the anti-apoptotic gene Bcl-2 and the embryo cleavage rate was significantly increased, while the proapoptotic gene Bax was significantly reduced. When 10 µg/ml UBA2 was added, the in vitro maturation rate, blastocyst rate, and SUMO-1 protein content of oocytes increased significantly (p < .05), and the expression of proapoptotic gene Caspase3 was significantly decreased (p < .05), while the viability of cumulus cells was extremely significantly reduced (p < .01). In summary, UBA2 can regulate the content of the SUMO-1 protein in mature pig oocytes in vitro, which in turn affects the maturation rate of oocytes, expression of apoptosis genes, cumulus cell viability, and the development of embryos after fertilization.