Integrated analysis of physiological, transcriptome, and metabolome analyses of the gills in Solenaia oleivora under ammonia exposure.

Ammonia is a common toxicant in aquatic systems and one of the key factors affecting aquaculture. However, data on mollusks' toxic response and coping mechanisms to ammonia nitrogen, especially freshwater mollusks, are still lacking. In this study, we evaluated the tolerance of a freshwater mollusk Solenaia oleivora to ammonia and investigated its coping mechanisms by combining physiological, metabolic, and transcriptomic analyses in the gills. The acute toxicity test revealed that the LC50-96 h (temperature-20 â„ƒ, pH-7.4) of ammonia in S. oleivora was 63.29 mg/L. The physiological and TUNEL results showed that although 10 mg/L ammonia exposure increased the activities of antioxidant, immune and ammonia detoxification-related enzymes, it still caused oxidative damage and cell apoptosis of gill tissues. A total of 97 differential metabolites (DMs) and 3431 differential expressed genes (DEGs) were identified after ammonia stress. Among them, most DMs and DEGs were involved in immune response, antioxidant, cell apoptosis, carbohydrate metabolism, amino acid metabolism, and lipid metabolism. The enhancement of glycolysis and lipid metabolisms may provide energy for immune response and ammonia detoxification. In addition, glutamine synthesis, alanine synthesis and urea cycle were involved in ammonia nitrogen detoxification in the gill tissue of S. oleivora. Our results indicate that ammonia leads to individual death in S. oleivora, as wells as oxidative damage, cell apoptosis, immune response, and metabolic changes of gill tissues. The findings will provide valuable information to assess the potential ecological risk of environmental ammonia to freshwater mollusks and theoretical guidance for the healthy aquaculture of S. oleivora.

Dual function of VGLL4 in muscle regeneration.

VGLL4 has previously been identified as a negative regulator of YAP. Here we show that VGLL4 regulates muscle regeneration in both YAP-dependent and YAP-independent manners at different stages. Knockout of VGLL4 in mice leads to smaller myofiber size and defective muscle contraction force. Furthermore, our studies reveal that knockout of VGLL4 results in increased muscle satellite cells proliferation and impaired myoblast differentiation, which ultimately leads to delayed muscle regeneration. Mechanistically, the results show that VGLL4 works as a conventional repressor of YAP at the proliferation stage of muscle regeneration. At the differentiation stage, VGLL4 acts as a co-activator of TEAD4 to promote MyoG transactivation and facilitate the initiation of differentiation in a YAP-independent manner. Moreover, VGLL4 stabilizes the protein-protein interactions between MyoD and TEAD4 to achieve efficient MyoG transactivation. Our findings define the dual roles of VGLL4 in regulating muscle regeneration at different stages and may open novel therapeutic perspectives for muscle regeneration.

Full-length transcriptome analysis provides new insights into the diversity of immune-related genes in the threatened freshwater shellfish Solenaia oleivora.

Solenaia oleivora, a valuable and rare bivalve endemic to China, is becoming a threatened freshwater sepcies. However, the lack of research on its genome and immune system will hinder advances in its conservation and artificial breeding. In this study, we obtained the full-length transcriptome of S. oleivora using PacBio sequencing. A total of 21,415 transcripts with an average length of 1,726 bp were generated. Among these transcripts, 12,084 had coding sequences (CDS), of which 8,639 were annotated in 6 databases. The structure analysis identified 625 transcript factors (TFs), 8,005 long non-coding RNAs (lncRNAs), and 5,288 simple sequences repeat (SSRs). Meanwhile, massive immune genes were identified from the transcriptome of S. oleivora. In terms of non-self-identification, 97 transcripts of pattern recognition receptors (PRRs) were discovered, including peptidoglycan recognition proteins (PGRPs), gram-negative bacteria binding proteins (GNBPs), toll-like receptors (TLRs), scavenger receptors (SRs), galectins (GALs), C-type lectins (CLTs), and fibrinogen-related protein (FREPs). For pathogen elimination, 7 transcripts related to antimicrobial peptides, lysozymes, and lysosomal enzymes were identified. Moreover, 33 complement-associated transcripts were found. This study enriched the genome resources of S. oleivora and provided new insights for the study of the immune system of S. oleivora.

In silico drug repositioning based on drug-miRNA associations.

Drug repositioning has become a prevailing tactic as this strategy is efficient, economical and low risk for drug discovery. Meanwhile, recent studies have confirmed that small-molecule drugs can modulate the expression of disease-related miRNAs, which indicates that miRNAs are promising therapeutic targets for complex diseases. In this study, we put forward and verified the hypothesis that drugs with similar miRNA profiles may share similar therapeutic properties. Furthermore, a comprehensive drug-drug interaction network was constructed based on curated drug-miRNA associations. Through random network comparison, topological structure analysis and network module extraction, we found that the closely linked drugs in the network tend to treat the same diseases. Additionally, the curated drug-disease relationships (from the CTD) and random walk with restarts algorithm were utilized on the drug-drug interaction network to identify the potential drugs for a given disease. Both internal validation (leave-one-out cross-validation) and external validation (independent drug-disease data set from the ChEMBL) demonstrated the effectiveness of the proposed approach. Finally, by integrating drug-miRNA and miRNA-disease information, we also explain the modes of action of drugs in the view of miRNA regulation. In summary, our work could determine novel and credible drug indications and offer novel insights and valuable perspectives for drug repositioning.

Emerging trends and hotspot in gut-lung axis research from 2011 to 2021: a bibliometrics analysis.

BACKGROUND: Increasing attention has been paid to the potential relationship between gut and lung. The bacterial dysbiosis in respiratory tract and intestinal tract is related to inflammatory response and the progress of lung diseases, and the pulmonary diseases could be improved by regulating the intestinal microbiome. This study aims to generate the knowledge map to identify major the research hotspots and frontier areas in the field of gut-lung axis. MATERIALS AND METHODS: Publications related to the gut-lung axis from 2011 to 2021 were identified from the Web of Science Core Collection. CiteSpace 5.7.R2 software was used to analyze the publication years, journals, countries, institutions, and authors. Reference co-citation network has been plotted, and the keywords were used to analyze the research hotspots and trends. RESULTS: A total of 3315 publications were retrieved and the number of publications per year increased over time. Our results showed that Plos One (91 articles) was the most active journal and The United States (1035 articles) published the most articles. We also observed the leading institution was the University of Michigan (48 articles) and Huffnagle Gary B, Dickson Robert P and Hansbro Philip M, who have made outstanding contributions in this field. CONCLUSION: The Inflammation, Infection and Disease were the hotspots, and the regulation of intestinal flora to improve the efficacy of immunotherapy in lung cancer was the research frontier. The research has implications for researchers engaged in gut-lung axis and its associated fields.

VGLL4 plays a critical role in heart valve development and homeostasis.

Heart valve disease is a major clinical problem worldwide. Cardiac valve development and homeostasis need to be precisely controlled. Hippo signaling is essential for organ development and tissue homeostasis, while its role in valve formation and morphology maintenance remains unknown. VGLL4 is a transcription cofactor in vertebrates and we found it was mainly expressed in valve interstitial cells at the post-EMT stage and was maintained till the adult stage. Tissue specific knockout of VGLL4 in different cell lineages revealed that only loss of VGLL4 in endothelial cell lineage led to valve malformation with expanded expression of YAP targets. We further semi-knockout YAP in VGLL4 ablated hearts, and found hyper proliferation of arterial valve interstitial cells was significantly constrained. These findings suggest that VGLL4 is important for valve development and manipulation of Hippo components would be a potential therapy for preventing the progression of congenital valve disease.

Hippo signaling is intrinsically regulated during cell cycle progression by APC/CCdh1.

The Hippo-YAP/TAZ signaling pathway plays a pivotal role in growth control during development and regeneration and its dysregulation is widely implicated in various cancers. To further understand the cellular and molecular mechanisms underlying Hippo signaling regulation, we have found that activities of core Hippo signaling components, large tumor suppressor (LATS) kinases and YAP/TAZ transcription factors, oscillate during mitotic cell cycle. We further identified that the anaphase-promoting complex/cyclosome (APC/C)Cdh1 E3 ubiquitin ligase complex, which plays a key role governing eukaryotic cell cycle progression, intrinsically regulates Hippo signaling activities. CDH1 recognizes LATS kinases to promote their degradation and, hence, YAP/TAZ regulation by LATS phosphorylation is under cell cycle control. As a result, YAP/TAZ activities peak in G1 phase. Furthermore, we show in Drosophila eye and wing development that Cdh1 is required in vivo to regulate the LATS homolog Warts with a conserved mechanism. Cdh1 reduction increased Warts levels, which resulted in reduction of the eye and wing sizes in a Yorkie dependent manner. Therefore, LATS degradation by APC/CCdh1 represents a previously unappreciated and evolutionarily conserved layer of Hippo signaling regulation.

Draft Genome Sequence of Alternaria longipes Causing Tobacco Brown Spot.

Alternaria is a cosmopolitan fungal genus associated with diverse hosts. Tobacco brown spot caused by Alternaria longipes is one of the most destructive diseases of tobacco. A. longipes can also infect many other plants, some animals and even humans. Here, we report a genome assembly of A. longipes CBS 540.94 using Oxford Nanopore Technologies. A total of 15 contigs were assembled, and the genome size was 37.5 Mb with contig N50 of 4.33 Mb. This genome resource will provide information for further research on comparative genomics of the genus Alternaria and be a valuable resource in investigations of the molecular interactions of pathogen and hosts.

Probing the Spin-Orbit Time Delay of Multiphoton Ionization of Kr by Bicircular Fields.

We study multiphoton ionization of Kr atoms by circular 400-nm laser fields and probe its photoelectron circular dichroism with the weak corotating and counterrotating circular fields at 800 nm. The unusual momentum- and energy-resolved photoelectron circular dichroisms from the ^{2}P_{1/2} ionic state are observed as compared with those from ^{2}P_{3/2} ionic state. We identify an anomalous ionization enhancement at sidebands related to the ^{2}P_{1/2} ionic state on photoelectron momentum distribution when switching the relative helicity of the two fields from corotating to counterrotating. By performing the two-color intensity-continuously-varying experiments and the pump-probe experiment, we find a specific mixed-photon populated resonant transition channel in counterrotating fields that contributes to the ionization enhancement. We then probe the time delay between the two spin-orbit coupled ionic states (^{2}P_{1/2} and ^{2}P_{3/2}) using bicircular fields and reveal that the resonant transition has an insignificant effect on the relative spin-orbit time delay.

LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments.

We describe LncACTdb 2.0 (http://www.bio-bigdata.net/LncACTdb/), an updated and significantly expanded database which provides comprehensive information of competing endogenous RNAs (ceRNAs) in different species and diseases. We have updated LncACTdb 2.0 with more data and several new features, including (i) manually curating 2663 experimentally supported ceRNA interactions from >5000 published literatures; (ii) expanding the scope of the database up to 23 species and 213 diseases/phenotypes; (iii) curating more ceRNA types such as circular RNAs and pseudogenes; (iv) identifying and scoring candidate lncRNA-associated ceRNA interactions across 33 cancer types from TCGA data; (v) providing illustration of survival, network and cancer hallmark information for ceRNAs. Furthermore, several flexible online tools including LncACT-Get, LncACT-Function, LncACT-Survival, LncACT-Network and LncACTBrowser have been developed to perform customized analysis, functional analysis, survival analysis, network illustration and genomic visualization. LncACTdb 2.0 also provides newly designed, user-friendly web interfaces to search, browse and download all the data. The BLAST interface is convenient for users to query dataset by inputting custom sequences. The Hot points interface provides users the most studied items by others. LncACTdb 2.0 is a continually updated database and will serve as an important resource to explore ceRNAs in physiological and pathological processes.

Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers.

Lnc2Cancer 2.0 (http://www.bio-bigdata.net/lnc2cancer) is an updated database that provides comprehensive experimentally supported associations between lncRNAs and human cancers. In Lnc2Cancer 2.0, we have updated the database with more data and several new features, including (i) exceeding a 4-fold increase over the previous version, recruiting 4989 lncRNA-cancer associations between 1614 lncRNAs and 165 cancer subtypes. (ii) newly adding about 800 experimentally supported circulating, drug-resistant and prognostic-related lncRNAs in various cancers. (iii) appending the regulatory mechanism of lncRNA in cancer, including microRNA (miRNA), transcription factor (TF), variant and methylation regulation. (iv) increasing more than 70 high-throughput experiments (microarray and next-generation sequencing) of lncRNAs in cancers. (v) Scoring the associations between lncRNA and cancer to evaluate the correlations. (vi) updating the annotation information of lncRNAs (version 28) and containing more detailed descriptions for lncRNAs and cancers. Moreover, a newly designed, user-friendly interface was also developed to provide a convenient platform for users. In particular, the functions of browsing data by cancer primary organ, biomarker type and regulatory mechanism, advanced search following several features and filtering the data by LncRNA-Cancer score were enhanced. Lnc2Cancer 2.0 will be a useful resource platform for further understanding the associations between lncRNA and human cancer.

ncRI: a manually curated database for experimentally validated non-coding RNAs in inflammation.

BACKGROUND: Inflammation has been considered to be central to the onset, progression, and outcome of infectious diseases, especially as one of the hallmarks of cancer. Non-coding RNAs (ncRNAs), such as miRNAs and lncRNAs, have emerged as vital regulators in control of immune and inflammatory processes, and also play important roles in the inflammatory disease and immunotherapy. RESULTS: In this study, we presented a database ncRI, which documented experimentally verified ncRNAs in inflammatory diseases, from published articles. Each entry contained the detailed information about ncRNA name, inflammatory diseases, mechanism, experimental techniques (e.g., microarray, RNA-seq, qRT-PCR), experimental samples (cell line and/or tissue), expression patterns of ncRNA (up-regulated or down-regulated), reference information (PubMed ID, year of publication, title of paper) and so on. Collectively, ncRI recorded 11,166 entries that include 1976 miRNAs, 1377 lncRNAs and 107 other ncRNAs across 3 species (human, mouse, and rat) from more than 2000 articles. All these data are free for users to search, browse and download. CONCLUSION: In summary, the presented database ncRI provides a relatively comprehensive credible repository about ncRNAs and their roles in inflammatory diseases, and will be helpful for research on immunotherapy. The ncRI is now freely available to all users at http://www.jianglab.cn/ncRI/.

Dissecting the m6A methylation affection on afatinib resistance in non-small cell lung cancer.

Non-small cell lung cancer (NSCLC) is one of the leading causes of cancer deaths. Afatinib is the first-line anti-cancer agent for treatment of NSCLC. However, unexpected resistance has been a major obstacle for its clinical efficacy. In this study, we dissected afatinib resistance from the perspective of N6-Methyladenosine (m6A) modification. First, we depicted the m6A modification profiles for the afatinib resistant and sensitive NSCLC cell lines (H1299 and A549). We found that the sum enrichment scores of the resistant cell line (H1299) was much higher than that of the sensitive cell line (A549). Next, we identified the functionally m6A-modified genes, which were the intersection of the differentially m6A methylated genes and the differentially expressed genes between H1299 and A549, as well as negative correlation between m6A modification levels and gene expression levels. In addition, functional enrichment analysis of the functionally m6A-modified genes indicated that m6A methylation might modify cell cycle to affect afatinib response. Furthermore, the functionally m6A-modified genes were over-represented in the putative drug resistance-associated genes and the FDA-approved drug targets, and had significantly higher average degree and clustering coefficient than other genes in protein-protein interaction (PPI) network. We also identified five network modules, which were all related to drug resistance functions. Finally, survival analysis demonstrated that m6A modification could affect prognosis of NSCLC patients. In conclusion, we conducted a first attempt to dissect m6A methylation affection on afatinib resistance in NSCLC, and brought inspiration for the study of epigenetic roles in drug resistance.

The TEA domain family transcription factor TEAD4 represses murine adipogenesis by recruiting the cofactors VGLL4 and CtBP2 into a transcriptional complex.

The Hippo signaling pathway is known to play an important role in multiple physiological processes, including adipogenesis. However, whether the downstream components of the Hippo pathway are involved in adipogenesis remains unknown. Here we demonstrate that the TEA domain family (TEAD) transcription factors are essential for adipogenesis in murine 3T3-L1 preadipocytes. Knockdown of TEAD1-4 stimulated adipogenesis and increased the expression of adipocyte markers in these cells. Interestingly, we found that the TEAD4 knockdown-mediated adipogenesis proceeded in a Yes-associated protein (YAP)/TAZ (Wwtr1)-independent manner and that adipogenesis suppression in WT cells involved formation of a ternary complex comprising TEAD4 and the transcriptional cofactors C-terminal binding protein 2 (CtBP2) and vestigial-like family member 4 (VGLL4). VGLL4 acted as an adaptor protein that enhanced the interaction between TEAD4 and CtBP2, and this TEAD4-VGLL4-CtBP2 ternary complex dynamically existed at the early stage of adipogenesis. Finally, we verified that TEAD4 directly targets the promoters of major adipogenesis transcription factors such as peroxisome proliferator-activated receptor γ (PPARγ) and adiponectin, C1Q, and collagen domain-containing (Adipoq) during adipogenesis. These findings reveal critical insights into the role of the TEAD4-VGLL4-CtBP2 transcriptional repressor complex in suppression of adipogenesis in murine preadipocytes.

Unifying Tunneling Pictures of Strong-Field Ionization with an Improved Attoclock.

We demonstrate a novel attoclock, in which we add a perturbative linearly polarized light field at 400 nm to calibrate the attoclock constructed by an intense circularly polarized field at 800 nm. This approach can be directly implemented to analyze the recent hot and controversial topics involving strong-field tunneling ionization. The generally accepted picture is that tunneling ionization is instantaneous and that the tunneling probability synchronizes with the laser electric field. Alternatively, recently it was described in the Wigner picture that tunneling ionization would occur with a certain of time delay. We unify the two seemingly opposite viewpoints within one theoretical framework, i.e., the strong-field approximation (SFA). We illustrate that both the instantaneous tunneling picture and the Wigner time delay picture that are derived from the SFA can interpret the measurement well. Our results show that the finite tunneling delay will accompany nonzero exit longitudinal momenta. This is not the case for the instantaneous tunneling picture, where the most probable exit longitudinal momentum would be zero.

D-lnc: a comprehensive database and analytical platform to dissect the modification of drugs on lncRNA expression.

Long non-coding RNAs (lncRNAs) have been proven to be implicated in the pathogenesis of various diseases. Multiple studies have demonstrated that small molecule drugs can modify lncRNA expression, which suggests a promising therapy for human diseases. Here, we constructed a comprehensive query and analytical platform D-lnc to dissect the influence of drugs on lncRNA expression. Firstly, we manually curated the experimentally validated regulations of drugs on lncRNA expression and recorded 7,825 entries between 59 drugs and 7,538 lncRNAs across five species from nearly 1,000 published papers. Secondly, we comprehensively screened the Connectivity Map (cMap) and the Gene Expression Omnibus (GEO) databases to obtain the drug-perturbed gene expression profiles. Through probe re-annotation of microarray data, we identified 19,946 putative associations between 1,279 drugs and 129 lncRNAs in cMap and 36,210 entries between 115 drugs and 2,360 lncRNAs in GEO. Finally, we developed an online analytical platform to predict the potential acting drugs or modified lncRNAs based on user input lncRNA sequence or drug structure through computing the similarities of lncRNA sequences or drug structures. In a word, D-lnc provides a comprehensive platform to detect the modification of drugs on lncRNA expression, which would facilitate the development of lncRNA-targeted therapeutics. D-lnc is freely available at http://www.jianglab.cn/D-lnc/ .

Shellfish polysaccharides: A comprehensive review of extraction, purification, structural characterization, and beneficial health effects.

Global food systems are currently facing great challenges, such as food sources, food safety, and environmental crises. Alternative nutritional resources have been proposed as part of the solution to meeting future global food demand. In the natural resources, shellfish are the major component of global aquatic animals. Although most studies focus on the allergy, toxin, and contamination of shellfish, it is also a delicious food to the human diet rich in proteins, polysaccharides, minerals, and omega-3. Among the functional ingredients, shellfish polysaccharides possess nutritional and medicinal values that arouse the great interest of researchers. The selection of the extraction approach and the experimental condition are the key factors that influence the extraction efficiency of shellfish polysaccharides. Importantly, the purification of crude polysaccharides comprises the enrichment of shellfish polysaccharides and isolation of fractions, also resulting in various structural characteristics and physicochemical properties. Chemical modification is also an efficient method to further improve the biological activities of shellfish polysaccharides. This review summarizes the extraction, purification, structural characterization, and chemical modification methods for shellfish polysaccharides. Additionally, the beneficial health effects of shellfish polysaccharides are highlighted, with an emphasis on their potential mechanism. Finally, current challenges and perspectives on shellfish polysaccharides are also spotlighted.

Rapid anaerobic culture and reaction kinetic study of anammox bacteria on microfluidic chip.

Anammox bacteria are being increasingly investigated as part of an emerging nitrogen removal technology. However, due to the difficulty in culturing, current understanding of their behavior is limited. In this study, anaerobic microfluidic chips were used to study anammox bacteria, showing great advantages over reactors. On-chip fluorescence in situ hybridization (FISH) showed the relative abundance of free form anammox bacteria increased by 56.1 % after one week's culture, an increase that is three times higher than that of bioreactor (17.1 %). For granular form cultures, the nitrogen removal load reached 2.34 âˆ¼ 2.51 kg-N/(m3·d), which was also substantially higher than the bioreactor (∼1.22 kg-N/(m3·d)). Furthermore, studying the kinetics of nitrite inhibition of granular sludge with different particle sizes (100-900 µm) showed that the maximum ammonia load and the nitrite semi-saturation coefficient noticeably decreased for smaller particle sizes. These results illustrate the usefulness of the microfluidic method for in-depth understanding anammox process and its implementation.

A study on the structure-functionality relationship of Solenaia oleivora protein under high-intensity ultrasonication processing.

Solenaia oleivora is a valuable freshwater mussel endemic to China with a high content of high-quality proteins, but the lack of structural information and limited functionality of Solenaia oleivora proteins constrained their application in the food industry. This study investigates the changes in structural characteristics and functionality of Solenaia oleivora protein under ultrasound processing at power from 200 to 600 W. The ultrasound treatment caused increased contents of ß-turn and α-helix, and the exposure of interior hydrophobic groups, resulting in the increased hydrophobicity by around 3 folds. The ultrasound treatment could significantly decrease particle size and increase surface charges of Solenaia oleivora proteins, facilitating the increase of hydrosolubility from 10.2% to 81.7%. These structural changes and increased hydrosolubility contributed to the enhancement of emulsifying and foaming properties, and in vitro digestibility. The results suggested that the ultrasound-treated Solenaia oleivora proteins possessed the potential as an alternative protein in food applications.

Chromosome-level genome assembly of the freshwater mussel Sinosolenaia oleivora (Heude, 1877).

Sinosolenaia oleivora (Bivalve, Unionida, Unionidae), is a near-endangered edible mussel. In 2022, it was selected by the Ministry of Agriculture and Rural Affairs as a top-ten aquatic germplasm resource, with potential for industrial development. Using Illumina, PacBio, and Hi-C technology, a high-quality chromosome-level genome of S. oleivora was assembled. The assembled S. oleivora genome spanned 2052.29 Mb with a contig N50 size of 20.36 Mb and a scaffold N50 size of 103.57 Mb. The 302 contigs, accounting for 98.41% of the total assembled genome, were anchored into 19 chromosomes using Hi-C scaffolding. A total of 1171.78 Mb repeat sequences were annotated and 22,971 protein-coding genes were predicted. Compared with the nearest ancestor, a total of 603 expanded and 1767 contracted gene families were found. This study provides important genomic resources for conservation, evolutionary research, and genetic improvements of many economic traits like growth performance.