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Counterfactual conditional is a common linguistic phenomenon in linguistics. This paper compares and analyzes Chinese-Vietnamese counterfactual conditional based on constructive grammar, and finds out the essential differences between them. This paper analyzes three typical Chinese constructive grammar [hypothetical conjunction+negator +a,b], [hypothetical conjunction+a,b], [早知道zao zhi dao+ a,b], and three typical Vietnamese constructive grammar[counterfactual marker+a,b],[đã/đã...rồi]，[hypothetical conjunction+a,b], and concludes that the Chinese and Vietnamese counterfactual conditionals are highly similar but with many distinctions. The main difference is that Chinese lacks mature counterfactual markers, while Vietnamese has obvious markers of counterfactual conditionals. which can also be used to realize the counterfactual meaning through negation, time and hypothetical conjunction.

Oral colon-targeted drug delivery systems (OCDDs) are designed to deliver the therapeutic agents to colonic disease sites to improve the effectiveness of drug treatment, increase bioavailability, and reduce systemic side effects and are beneficial for the treatment of colorectal cancer (CRC) and inflammatory bowel disease (IBD). However, concerns about the biosafety of OCDDs are increasing, and changes in the physiological environment of the gastrointestinal tract can affect the therapeutic efficacy of the drug. Herein, we report about an orally administered colon-accumulating mitochondria-targeted drug delivery nanoplatform (M27-39@FA-MCNs), which was synthesized using the small peptide, M27-39, and folic acid (FA)-modified mesoporous carbon nanoparticles (FA-MCNs). The phenolic resin polymerized with phloroglucinol and formaldehyde (PF) was used for fabricating MCNs using a one-step soft-template method. Folic acid (FA) can be covalently combined with chitosan-modified MCNs to obtain FA-MCNs. The M27-39@FA-MCNs were stable with a spherical morphology and an average diameter of 129 nm. The cumulative release rate of M27-39@FA-MCNs in the artificial gastric fluid (pH = 1.2) and intestinal fluid (pH = 6.8) for 6 h was 87.77%. This nanoplatform maintains the advantages of both FA and MCNs to improve the bioactivity of M27-39 with high drug accumulation in colorectal tumor tissues and the ease of excretion, thus ameliorating its biosafety and targetability. Furthermore, M27-39@FA-MCNs induced tumor-cell apoptosis and inhibited tumor growth by disrupting mitochondrial energy metabolism and regulating the mitochondrial apoptosis signaling pathway and immune inflammatory response. Thus, such a mitochondria-targeting FA-modified nanoplatform based on mesoporous carbon and a bioactive peptide may provide a precise strategy for CRC treatment. STATEMENT OF SIGNIFICANCE: In this study, we constructed an orally administered colon-accumulating mitochondria-targeted drug delivery nanoplatform (M27-39@FA-MCNs), which was synthesized using the small peptide (M27-39) and folic acid-modified mesoporous carbon nanoparticles (FA-MCNs). M27-39@FA-MCNs increased the targeting ability of M27-39 toward mitochondria and colon based on the properties of FA-MCNs; they also increased M27-39 accumulation and residence time in colon tumors. Oral administration of M27-39@FA-MCNs remarkably alleviated colorectal cancer (CRC) by targeting tumor cell mitochondria and interfering with the mitochondrial energy metabolism process, and inducing apoptosis related P53/Caspase-3 mitochondrial pathway activation. Therefore, M27-39@FA-MCNs may provide a safe and precise therapeutic strategy for CRC.

With the increasingly serious drug resistance of Acinetobacter baumannii, there is an increasingly urgent need for new antibacterial drugs. Phage lysin PlyAB1 has a bactericidal effect on drug-resistant A. baumannii, which has the potential to replace antibiotics to fight infection caused by A. baumannii. However, its application is limited by its thermal stability and lytic activity. To solve these problems, molecular dynamics (MD) simulations combined with Hotspot wizard 3.0 were used to identify key residue sites affecting thermal stability, and evolutionary analysis combined with multiple sequence alignment was used to identify key residue sites affecting lytic activity. Four single-point variants with significantly increased thermal stability and four single-point variants with significantly lytic activity were obtained, respectively. Furthermore, by superimposing mutations, we obtained three double-point variants, G100Q/K69R, G100R/K69R, and G100K/K69R, with significantly improved thermal stability and improved lytic activity. At 45°C, the lytic activity and half-life of the optimal variant G100Q/K69R were 1.51- and 24-fold higher than those of the wild PlyAB1, respectively. These results deepen our understanding of the structure and function of phage lysin and contribute to the application of phage lysin in antibiotic substitution.

Increasing evidence suggests that interspecific hybridization is crucial to speciation. However, chromatin incompatibility during interspecific hybridization often renders this process. Genomic imbalances such as chromosomal DNA loss and rearrangements leading to infertility have been commonly noted in hybrids. The mechanism underlying reproductive isolation of interspecific hybridization remains elusive. Here, we identified that modification of maternally defined H3K4me3 in Xenopus laevis and Xenopus tropicalis hybrids determines the different fates of the two types of hybrids as te×ls with developmental arrest and viable le×ts. Transcriptomics highlighted that the P53 pathway was overactivated, and the Wnt signaling pathway was suppressed in te×ls hybrids. Moreover, the lack of maternal H3K4me3 in te×ls disturbed the balance of gene expression between the L and S subgenomes in this hybrid. Attenuation of p53 can postpone the arrested development of te×ls. Our study suggests an additional model of reproductive isolation based on modifications of maternally defined H3K4me3.

Coronaviruses are single-stranded, positive-sense RNA viruses that can infect many mammal and avian species. The Spike (S) protein of coronaviruses binds to a receptor on the host cell surface to promote viral entry. The interactions between the S proteins of coronaviruses and receptors of host cells are extraordinarily complex, with coronaviruses from different genera being able to recognize the same receptor and coronaviruses from the same genus able to bind distinct receptors. As the coronavirus disease 2019 pandemic has developed, many changes in the S protein have been under positive selection by altering the receptor-binding affinity, reducing antibody neutralization activities, or affecting T-cell responses. It is intriguing to determine whether the selection pressure on the S gene differs between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other coronaviruses due to the host shift from nonhuman animals to humans. Here, we show that the S gene, particularly the S1 region, has experienced positive selection in both SARS-CoV-2 and other coronaviruses. Although the S1 N-terminal domain exhibits signals of positive selection in the pairwise comparisons in all four coronavirus genera, positive selection is primarily detected in the S1 C-terminal domain (the receptor-binding domain) in the ongoing evolution of SARS-CoV-2, possibly owing to the change in host settings and the widespread natural infection and SARS-CoV-2 vaccination in humans.

Supplementary Tables - Supplementary Tables S1-3. Table S1. List of quantitative RT-PCR primers used in this study; Table S2. List of ChIP-qPCR primers used in this study; Supplementary Table S3. Distribution of H3K9me3 ChIP-seq peaks in various types of human cancer cells. Supplementary Figures - Supplementary Figures S1-7. Supplementary Figure S1. Enrichment profile plots of the KDM4B-dependent H3K9me3 peaks overlapped SINE, LTR, genebody and intergenic in three cell types; Supplementary Figure S2. The LINE-1 phylogenetic tree and the evaluation of H3K9me3 signal in selected evolutionarily young LINE-1 element; Supplementary Figure S3. Effect of KDM4 proteins on LINE-1 expression; Supplementary Figure S4. Schematic illustration of retrotransposition cassette assay; Supplementary Figure S5. The ORF1p, global H3K9me3 and DNA damage level were detected in various breast cell lines; Supplementary Figure S6. The retrotransposition cassette assay in breast cancer cells and normal breast epithelial cells; Supplementary Figure S7. ORF2 expression is sufficient to induce the DNA damage.

Background:: Sini decoction (SND) is a widely used Traditional Chinese Medicine (TCM). The reports of SND application in colorectal cancer (CRC) is limited. Objective:: The objective of this study is to investigate the anti-tumor activity of SND in the treatmeant of CRC Methods:: SND was analyzed using high-performance liquid chromatography. A CRC metastasis model was established using murine CT-26 cells. Whole-body fluorescence imaging was used to observe CRC liver metastasis. Liver morphology was determined using hematoxylin-eosin staining. Cytokine mRNA expression (interleukin-2 (IL-2), interleukin-10 (IL-10), interferon-gamma (IFN-γ), and tumor necrosis factor beta (TNF-β)) were determined using real-time reverse transcription polymerase chain reaction. Spectral flow cytometry was used to detect mouse tumor immune subgroups. Databases were used to find potential target genes of SND. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were used to identify potential signaling pathways of target genes. Results:: SND suppressed CRC liver metastasis and alleviated liver injury in vivo. After SND treatment, IL-2 and IFN-γ were upregulated, whereas IL-10 and TGF-β were downregulated. Moreover, CD3+, CD8+T cells, natural killer T cells, and macrophages increased significantly after SND treatment, while CD4+CD25+T cells decreased significantly. Importantly, increasing the aconite concentration had a better anti-tumor effect. Fifty-50 compounds in SND were screened, and 611 potential target genes were identified. Functional analyses showed that the genes were associated with the PI3K-Akt signaling pathway, EGFR tyrosine kinase inhibitor resistance, and HIF-1 signaling pathway. Conclusion:: SND exerts anti-tumor activity by inhibiting tumor progression and enhancing anti-tumor immunity in mice, suggesting its application to prevent and treat CRC. conclusion: SND exerts its anti-tumor activity by inhibiting tumor progression and enhancing the anti-tumor immune response in mice. SND could be used as a drug to prevent and treat for colon cancer. other: none

Background: Given the apparent benefits, the implementation of early ambulation is becoming increasingly important in spinal surgery. The timing for patients first time get out of bed for ambulation after spinal surgery has a wide range. Since Jan 2022, we conducted a study of early ambulation (ambulated within 4h postoperatively) in elderly patients following long-segments lumbar decompression and fusion surgery. In order to better understand elderly patients’ perceptions of the early ambulation, clarify controversies, and ultimately contribute to the improvement of elderly patients’ perioperative experience and also the quality of life, we carried out this qualitative approach. Methods: A qualitative description design with face-to-face semi-structured interviews was used. Twenty-four patients were enrolled in participating and completing this qualitative investigation from February to June 2022. Interviews were audio-recorded, and content analysis was used for data analysis. Results: Six themes were identified from this study about patient’s experience and concerns on early ambulation: Worries, Benefits, Daily Routines, Pain, Education and Supports. The findings showed the obstacles in early ambulation practice and highlighted the importance of education on early ambulation in the perioperative hospitalization. Conclusions: Unequivocal guidance for early ambulation and multidisciplinary ambulation protocol, including comprehensive pain management plan are essential to induce patient education, which may have positive effects on reducing stress and getting rid of anxiety for postoperative early ambulation.

The Guided bone regeneration (GBR) technique is the most common and durable approach to repairing bone defects in periodontal surgery. However, membrane exposure causes bacterial infiltration, which lowers the functional integrity of the barrier membrane and destroys bone repair. Here, an antibacterial peptide-modified small intestinal submucosa (SIS) membrane is used as a new GBR membrane for effective bone regeneration. The peptide JH8194 was placed into chitosan microspheres to preserve its stability and allow for sustained release, which realizes rapid and efficient functional modification of the SIS membrane. Biocompatibility and certain antibacterial activities were found in the modified SIS membrane (SIS@CS-JH8194). Additionally

Hepatocellular carcinoma (HCC) is one of the most malignant tumors worldwide and HCC patients often develop drug resisitene. Long non-coding RNAs (LncRNAs) are closely related to cell cycle, growth, development, differentiation, and apoptosis. Abnormally expressed lncRNAs have been proved to mediate drug resistance in tumor cells. However, the effect of LIMT on drug resistance has not been explored in HCC. In this study, we explored the effect of long non-coding RNA LIMT on drug resistance and its underlying mechanism in hepatocellular carcinoma (HCC). Our results showed that LncRNA LINC01089 (LIMT) expression is downregulated in 78.57% (44/56) of 56 HCC tumor tissue samples. LIMT expression is also downregulated in HCC cells compared with that in normal liver LO2 cells. Inhibition of LIMT increases the resistance to sorafenib and promotes cell invasion via regulation of epithelial to mesenchymal transition (EMT) in HCC. StarBase V3.0 was used to predict the potential binding site of miR-665 in . Furthermore, miR-665 participates in sorafenib resistance and also regulates the level of EMT-related proteins in HCC cells. A rescue experiment demonstrated that silencing of eliminats the inhibitory effect of the miR-665 inhibitor on sorafenib resistance in HCC cells. Taken together, our findings revealed that downregulation of LIMT increases the resistance of HCC to sorafenib via miR-665 and EMT. Therefore, LIMT, which serves as a therapeutically effective target, will provide new hope for the treatment of HCC.

Titanium dioxide (TiO2), as a representative of metallic oxides, is widely used as food additive to serve as coloring or antibacterial packaging fortifier. However, in recent years, the potential hazards of nano-sized TiO2 food additives to human beings is still in doubt. In this work, we systematically studied the interactions between three sizes of TiO2 particles and the cell membrane systems with confocal laser scanning microscopy. We used both giant unilamellar vesicles and human colon cancer cells to mimic actual cell membrane systems. The results demonstrate the strong effect of particle size on membrane disruption and leakage behaviors. Among the three sizes of TiO2 nanoparticles (NPs) used in this work, the TiO2 NPs with the size of 110-300 nm are safe. In contrast, NPs with the size of 10-30 nm and 50-100 nm will cause the rupture and leakage of cell membranes. These indicates that the cytotoxicity of nano-sized TiO2 particles increases with the decrease of particle sizes. In addition, it is found that the size effect of TiO2 particles further depends on the membrane charge state. Simulations were also introduced to understand the results. This study would provide a theoretical basis for the production designing and safety standard of metallic oxide food additives.

Carbon nanomaterials such as fullerenes (C60) and graphene oxide (GO) are considered as promising candidates for diverse applications in biotechnology and biomedicine. However, their potential toxic effects are still under debate. Herein, by using melittin (Mel), a representative pore-forming peptide, as a testing molecule we demonstrated that even the low-concentrated (usually assumed non-toxic) C60 and GO could still mechanically perturb a cell membrane by adsorption and insertion, and consequently influence the function realization of membrane active proteins/peptides. Such perturbations, however, are particle-property and membrane-environment dependent. GO would sensitize both model bilayers and bacterial membranes to Mel, demonstrated as significantly enhanced membrane permeabilization ability or improved antibacterial performance of Mel. In contrast, C60 activates the permeabilization effect of Mel on model membranes, while produces exactly the reverse effect on living bacteria and mammalian cells. Simulations further provide molecular details of the structural disturbance and probe the residue-specific formation of C60-Mel complex in membrane. This work emphasizes the dependence of biological toxicity of nanomaterials on their physico-chemical properties, provides a facile method to detect the subtle structural perturbation of cell membranes at nanoscale, and suggests a necessity for a careful evaluation of the potential influences of nanomaterials on biological processes.

The Gram-negative bacterium Cytophaga hutchinsonii digests cellulose through a novel cellulose degradation mechanism. It possesses the lately characterized type IX secretion system (T9SS). We recently discovered that N-glycosylation of the C-terminal domain (CTD) of a hypothetical T9SS substrate protein in the periplasmic space of C. hutchinsonii affects protein secretion and localization. In this study, green fluorescent protein (GFP)-CTD(Cel9A) recombinant protein was found with increased molecular weight in the periplasm of C. hutchinsonii. Site-directed mutagenesis studies on the CTD of cellulase Cel9A demonstrated that asparagine residue 900 in the D-X-N-X-S motif is important for the processing of the recombinant protein. We found that the glycosyltransferase-related protein GtrA (CHU_0012) located in the cytoplasm of C. hutchinsonii is essential for outer membrane localization of the recombinant protein. The deletion of gtrA decreased the abundance of the outer membrane proteins and affected cellulose degradation by C. hutchinsonii. This study provided a link between the glycosylation system and cellulose degradation in C. hutchinsonii. IMPORTANCE N-Glycosylation systems are generally limited to some pathogenic bacteria in prokaryotes. The disruption of the N-glycosylation pathway is related to adherence, invasion, colonization, and other phenotypic characteristics. We recently found that the cellulolytic bacterium Cytophaga hutchinsonii also has an N-glycosylation system. The cellulose degradation mechanism of C. hutchinsonii is novel and mysterious; cellulases and other proteins on the cell surface are involved in utilizing cellulose. In this study, we identified an asparagine residue in the C-terminal domain of cellulase Cel9A that is necessary for the processing of the T9SS cargo protein. Moreover, the glycosyltransferase-related protein GtrA is essential for the localization of the GFP-CTD(Cel9A) recombinant protein. Deletion of gtrA affected cellulose degradation and the abundance of outer membrane proteins. This study enriched the understanding of the N-glycosylation system in C. hutchinsonii and provided a link between N-glycosylation and cellulose degradation, which also expanded the role of the N-glycosylation system in bacteria.

Background β-Farnesene is a sesquiterpene with versatile industrial applications. The production of β-farnesene from waste lipid feedstock is an attractive method for sustainable production and recycling waste oil. Yarrowia lipolytica is an unconventional oleaginous yeast, which can use lipid feedstock and has great potential to synthesize acetyl-CoA-derived chemicals. Results In this study, we engineered Y. lipolytica to produce β-farnesene from lipid feedstock. To direct the flux of acetyl-CoA, which is generated from lipid β-oxidation, to β-farnesene synthesis, the mevalonate synthesis pathway was compartmentalized into peroxisomes. β-Farnesene production was then engineered by the protein engineering of β-farnesene synthase and pathway engineering. The regulation of lipid metabolism by enhancing β-oxidation and eliminating intracellular lipid synthesis was further performed to improve the β-farnesene synthesis. As a result, the final β-farnesene production with bio-engineering reached 35.2 g/L and 31.9 g/L using oleic acid and waste cooking oil, respectively, which are the highest β-farnesene titers reported in Y. lipolytica. Conclusions This study demonstrates that engineered Y. lipolytica could realize the sustainable production of value-added acetyl-CoA-derived chemicals from waste lipid feedstock.

Genome reduction has been emerged as a powerful tool to construct ideal chassis for synthetic biology. Random genome reduction couple genomic deletion with growth and has the potential to construct optimum genome for a given environment. Recently, we developed a transposon-mediated random deletion (TMRD) method that allows the random and continuous reduction of Escherichia coli genome. Here, to prove its ability in constructing optimal cell factories, we coupled polyhydroxybutyrate (PHB) accumulation with random genome reduction and proceeded to reduce the E. coli genome. Five mutants showed high biomass and PHB yields were selected from 18 candidates after ten rounds of genome reduction. And eight or nine genomic fragments (totally 230.1–270.0 Kb) were deleted in their genomes, encompassing 4.95%–5.82% of the parental MG1655 genome. Most mutants displayed better growth, glucose utilization, protein expression, and significant increase of electroporation efficiency compared with MG1655. The PHB content and concentration enhanced up to 13.3%–37.2% and 60.2%–102.9% when batch fermentation was performed in M9-glucose medium using the five mutants. Particularly, in mutant H16, lacking 5.28% of its genome, the increase of biomass and PHB concentration were more than 50% and 100% compared with MG1655, respectively. This work expands the strategy for creating streamlined chassis to improve the production of high value-added products.

Background Salmonella is a common foodborne pathogen, which can cause intestinal diseases. In the last decades, the overuse of antibiotics has led to a pandemic of drug-resistant bacterial infections. To tackle the burden of antimicrobial resistant pathogens, it is necessary to develop new antimicrobial drugs with novel modes of action. However, the research and development of antibiotics has encountered bottlenecks, scientific hurdles in the development process, as well as safety and cost challenges. Phages and phage endolysins are promising antibacterial agents that can be used as an alternative to antibiotics. In this context, the expression of endolysin derived from different phages through microbial cells as a chassis seems to be an attractive strategy. Results In this study, a new endolysin from the Salmonella phage XFII-1, named XFII, was screened and obtained. The endolysin yield exceeded 100 mg/mL by heterologous expression from E. coli BL21 and short induction. The endolysin XFII exhibited high bactericidal activity at a concentration of 0.5 μg/mL and reduced the OD600 nm of EDTA-pretreated E. coli JM109 from 0.8 to 0.2 within 5 min. XFII exhibited good thermo-resistance, as it was very stable at different temperatures from 20 to 80℃. Its bactericidal activity could keep constant at 4 °C for 175 days. In addition, the endolysin was able to exert lytic activity in eutrophic conditions, including LB medium and rabbit serum, and the lytic activity was even increased by 13.8% in 10% serum matrices. XFII also showed bactericidal activity against many Gram-negative bacteria, including Salmonella, E. coli, Acinetobacter baumannii, and Klebsiella pneumoniae. Surprisingly, the combination of endolysin XFII and chitosan showed a strong synergy in lysing E. coli and Salmonella without EDTA-pretreatment, and the OD600 nm of E. coli decreased from 0.88 to 0.58 within 10 min. Conclusions The novel globular endolysin XFII was screened and successfully expressed in E. coli BL21. Endolysin XFII exhibits a broad lysis spectrum, a rapid and strong bactericidal activity, good stability at high temperatures and under eutrophic conditions. Combined with chitosan, XFII could spontaneously lyse Gram-negative bacteria without pretreatment. This work presented the first characterization of combining endolysin and chitosan in spontaneously lysing Gram-negative bacteria in vitro.

We aimed to evaluate whether the buddy balloon technique (BBT) is superior to the buddy wire technique (BWT) with regard to the accuracy of stent placement during percutaneous coronary intervention (PCI).We enrolled patients who had been identified with significant stent movement before the stent was dilated at five hospitals and were randomly converted to either the BBT or BWT technique. The primary endpoints were the incidence of technical success and major adverse cardiovascular events (cardiac death, myocardial infarction, target lesion revascularization, and in-stent restenosis) at 2 years of follow-up. The secondary endpoints were the contrast volume used for the procedure and the total procedural time.From August 2018 to July 2019, 66 patients were enrolled, with 33 patients in each group. All patients were successfully followed up to 2 years. At the primary endpoints, compared with patients treated using BWT, those in the BBT group showed significantly better technical success (93.94% versus 39.39%, respectively; P0.0001). There was no significant difference in the incidence of major cardiovascular adverse events (6.06% versus 12.12%, respectively; P = 0.392). At the secondary endpoints, the contrast volume used for the procedure was lower with BBT (85.97 ± 22.45 versus 115.00 ± 21.45 mL, respectively; P0.0001); similarly, the total procedural time was shorter with BBT (65.94 ± 12.14 versus 74.33 ± 15.36 minutes, respectively; P0.0001).BBT could better restrict stent movement and facilitate precise stent deployment, with significant superiority over BWT. In addition, BBT can reduce the procedural time and contrast dose.

A method for gram-scale synthesis of graphitic carbon nitride quantum dots (g-C

The hypoxic microenvironment contributes to the chemoresistance of many malignant tumors including colorectal cancer (CRC). Accumulating studies have indicated that long non-coding RNAs (lncRNAs) play important roles in chemotherapy resistance. In this study, we aimed to determine the effect of lncRNAs in hypoxia-mediated resistance in CRC and its potential mechanism. Here, we discovered that hypoxia-induced oxaliplatin resistance and HOX transcript antisense RNA (HOTAIR) expression was increased in hypoxia-treated CRC cell lines and CRC tumors. Knockdown of HOTAIR by siRNA reduced the viability and proliferation of CRC cells treated with oxaliplatin and reversed hypoxia-induced resistance. Mechanically, we found that HOTAIR modulates zinc finger E-box binding homeobox 1 (ZEB1) expression by negative regulations of miR-1277-5p. When miR-1277-5p was silenced, knockdown of HOTAIR was unable to reduce the oxaliplatin resistance in CRC cells. In mouse models of CRC, HOTAIR knockdown markedly inhibited the tumor growth when treated with oxaliplatin. Thus, HOTAIR/miR-1277-5p/ZEB1 axis appears a promising therapeutic target for improving the oxaliplatin efficacy in CRC.

Genome reduction has been emerged as a powerful tool to construct ideal chassis for synthetic biology. Random genome reduction couple genomic deletion with growth and has the potential to construct optimum genome for a given environment. Recently, we developed a transposon-mediated random deletion (TMRD) method that allows the random and continuous reduction of

Background The concept of multi-step progression from atypical adenomatous hyperplasia (AAH) to invasive adenocarcinoma (ADC) has been proposed, and ground-glass nodules (GGNs) may play a critical role during the early lung tumorigenesis. We present the first comprehensive description of the genomic architecture of GGNs to unravel the genetic basis of GGN. Methods We investigated 30 GGN-like lungs ADC by performing >1,000× whole-exome sequencing (WES) and characterized the genomic variations and evaluate the relationship between the clinicopathologic and molecular characteristics in this disease. Results Despite the low somatic mutation burden, GGNs exhibited high intratumor heterogeneity (ITH) characterized by the proportion of subclonal mutations. Different mutagenesis shaped the genomes of GGN during cancer evolution and were mostly featured by molecular clock-like signatures that occur in clonal mutations and defective DNA mismatch signatures that occur in subclonal mutations. Moreover, 10.7-67.1% clonal mutations occurred after whole-genome doubling (WGD), indicating that WGD could be a frequent truncal event in GGNs. Samples with WGD showed higher genomic instability but lower ITH. These GGNs were characterized by recurrent focal copy-number changes that are highly associated with tumorigenesis, with only two genes (EGFR and RBM10) that were recurrently mutated. Additionally, GGNs with different pathological subtypes or computed tomography (CT) features exhibited distinct genetic characteristics. Lepidic predominant or pure GGNs in CT images carried a lower mutation burden and had a relatively stable genome than nonlepidic or mixed GGNs. GGNs with RBM10 mutations tended to accompany a pathologically lepidic pattern, indicating RBM10 may drive the distinct subtype of lung cancer with better prognosis. Conclusions These findings facilitated interpreting the genomic characteristics of GGNs, provided insight into the early stages of lung cancer evolution, and possessed potential clinical significance.

Plasmon-assisted reactions have different reaction mechanisms than conventional chemical reactions occurring in solutions, and the hot electrons produced by plasmon decay play an irreplaceable role...

Buffering exogenous perturbation is crucial to maintain transcriptional homeostasis during development. While miRNAs have been speculated to play a role in stability maintenance, previous studies seeking to check this conjecture focused on measurements of transcript levels at steady state or involved individual miRNA targets. We measured whole-genome expression dynamics by introducing a transient perturbation and establishing a perturbation and recovery system in Drosophila larvae. We inhibited all transcription and assayed transcriptomes at several time points during recovery from inhibition. We performed these experiments in the wild type and miRNA-deficient genetic backgrounds. Consistent with theories about miRNAs’ function in stabilizing the transcriptome, we find that attenuating miRNA expression leads to weak impairment in degradation of targets but strong destabilization of target genes when transcription is re-activated. We further fitted a model that captures the essential aspects of transcription dynamics in our experiments and found that the miRNA target transcripts uniformly overshoot the original steady state as they recover from a general inhibition of transcription if global miRNA levels are reduced. Collectively, our results provide experimental evidence for the idea that miRNAs act cumulatively to stabilize the transcriptional regulatory network. We therefore found a promising approach to assess the effect of these molecules on transcription dynamics.

With the rapid development of synthetic biology, the oleaginous yeast Yarrowia lipolytica has become an attractive microorganism for chemical production. To better optimize and reroute metabolic pathways, we have expanded the CRISPR-based gene expression toolkit of Y. lipolytica. By sorting the integration sites associated with high expression, new neutral integration sites associated with high expression and high integration efficiency were identified. Diverse genetic components, including promoters and terminators, were also characterized to expand the expression range. We found that in addition to promoters, the newly characterized terminators exhibited large variations in gene expression. These genetic components and integration sites were then used to regulate genes involved in the lycopene biosynthesis pathway, and different levels of lycopene production were achieved. The CRISPR-based gene expression toolkit developed in this study will facilitate the genetic engineering of Y. lipolytica.

Genome reduction is an important strategy in synthetic biology for constructing functional chassis cells or minimal genomes. However, the limited knowledge of complex gene functions and interactions makes genome reduction by rational design encounter a bottleneck. Here, we present an iterative and random genome reduction method for

The Musca domestica larvae are well known for its multifunctions and great nutritional value. The present study aimed at investigating the beneficial effect of Musca domestica larvae extract (Mde) against memory impairment, structural damage and oxidative stress in aged rats. Twenty-month-old rats were gavaged with Mde for 2 mo. Morris Water Maze test indicated Mde prevented aging-induced spatial learning and memory dysfunction in the aged rats. Mde supply was also found to attenuate age-associated changes of brain histology that observed by light microscopy and transmission electron microscopy. Moreover, the increase of antioxidant capacity, glutathione peroxidase (GPx) activity, superoxide dismutase (SOD) activity, as well as the decreased methane dicarboxylic aldehyde (MDA) levels, were consistent with these results. Hence, we propose that oral administration of Mde could improve memory impairment via antioxidant action, and Mde has the potential to act as an excellent food supplement or medicine for the attenuation of brain aging.

Aluminum electrolytic capacitor (AEC) is one of the most age-affected components in ac–dc conversion, and its equivalent series resistance ( ESR ) is an important index for reflecting the healthy condition of AEC. In AEC-used boost power factor correction (PFC) converters, ESR of AEC causes a small jump in the switching ripple of output voltage at switching moments, especially at turn- off moments. This small jump is hardly observed at line-frequency scale, either using time-domain analysis or frequency-domain analysis. However using time–frequency analysis this jump is very prominent due to its singularity. In this article, an online ESR estimation method of AEC is proposed by using the wavelet transform (WT) based time–frequency analysis. The relationship between ESR and the jump amount of output voltage at turn- off moments is analyzed first, and then the ESR calculation model is derived using WT with the wavelet basis of the first derivative of Gaussian function. An appropriate sampling interval for the output voltage and the inductor current is determined. Besides, the online ESR estimation scheme is implemented including the hardware and software designs. Furthermore, a prototype of boost PFC converter with 220 V ac input and 360 V dc output is built, where an average current mode control chip UC3854 is used. Four factors are discussed for estimation accuracy in the experiment, and the estimated results are consistent with the results measured by LCR meter with a relative error less than 10%.

Gold nanoparticles have received widespread attention as surface-enhanced Raman scattering (SERS) detection active substrates. In this work, we used the nematic liquid crystal molecule N-(4-methoxybenzylidene)-4-butylaniline (MBBA) at room temperature to synthesize liquid crystal (LC)-Au nanoparticles in one step without adding any other reducing agents or stabilizers. Gold nanoparticles synthesized by this method have good sensitivity and stability as a SERS substrate. The nanoparticles can detect Rhodamine 6G (R6G) molecules with a concentration as low as 10−8 M, and the SERS signal does not decrease significantly in 30 days. Using this synthesis principle, we grew gold nanoparticles in a capillary in one step. We expect the proposed method to result in a highly efficient and portable SERS substrate after subsequent improvements.

4,4’-Dithiobisbenzoic acid (DTBA) is equivalent to two 4-mercaptobenzoic acid (pMBA) molecules connected together after losing H+, and this bimolecular mechanism of DTBA efficiently promotes the ionization reaction. Under the irradiation of laser light, DTBA molecules are broken to form bimolecules similar to pMBA, and this kind of bimolecular coupling greatly increases the probability of binding with Ag NPs. Also, this molecule has the carboxylic acid group, which leads to a certain sensitivity to pH. In this article, through the comparison of DTBA and pMBA parallel experiments, it is clear that DTBA has better Raman activity, higher reaction efficiency, and more stable reaction than pMBA. The occurrence of this highly efficient ionization reaction under the monitoring of surface-enhanced Raman spectroscopy (SERS) provides a certain value for the progress of further related reactions, and it also has a wide range of applications in pH sensors and intracellular pH monitoring.

Plateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai-Tibet Plateau. This extreme living environment makes it a great model to study animal adaptation to hypoxia, low temperature, and high carbon dioxide concentration. We provide an integrated resource, ZokorDB, for tissue specific regulatory network annotation for zokor. ZokorDB is based on a high-quality draft genome of a plateau zokor at 3,300 m and its transcriptional profiles in brain, heart, liver, kidney, and lung. The conserved non-coding elements of zokor are annotated by their nearest genes and upstream transcriptional factor motif binding sites. ZokorDB provides a general draft gene regulatory network (GRN), i.e., potential transcription factor (TF) binds to non-coding regulatory elements and regulates the expression of target genes (TG). Furthermore, we refined the GRN by incorporating matched RNA-seq and DNase-seq data from mouse ENCODE project and reconstructed five tissue-specific regulatory networks. A web-based, open-access database is developed for easily searching, visualizing, and downloading the annotation and data. The pipeline of non-coding region annotation for zokor will be useful for other non-model species. ZokorDB is free available at the website (bigd.big.ac.cn/zokordb/).

This study investigated the flavonoid compounds in Actinidia chinensis and Actinidia arguta fruits. A total of 125 flavonoids, including 9 anthocyanins, 12 catechins, 17 flavanones, 48 flavones (including 14 flavone C-glycosides), 29 flavonols, 6 isoflavones, and 4 proanthocyanidins, were identified in “Hongyang” kiwifruit (red flesh), “Jintao” kiwifruit, “Mini Amethyst” kiwiberry (purple flesh), and “Kuilv” kiwiberry. Thirty-nine metabolites showed significantly different contents between “Hongyang” and “Jintao,” and 38 of them showed higher content in “Hongyang,” whereas 39 metabolites showed significantly different contents between “Mini Amethyst” and “Kuilv,” and 31 of them showed higher content in “Mini Amethyst.” This result indicates the superior nutritional value of the pigmented kiwi cultivars in terms of flavonoids. Multivariate statistical analysis indicates that the variation in flavonoid profiles contributes to the pigmentation phenotypes of “Hongyang” and “Mini Amethyst.” Further comparative transcriptomic analysis revealed that structural genes in the anthocyanin synthesis pathway (AcF3H, AcF3′H, AcDFR, AcUFGT) and transcription factors (AcMYB10, AcbHLH5) may be involved in the pigmentation of the red-fleshed A. chinensis, whereas AaF3H, AaF3GT, and AaMYB110 may play important roles in the pigmentation of the purple-fleshed A. arguta. This study provides broader insight into the variation in flavonoid profiles among kiwifruit/berry, evaluates the flavonoid nutrition of the four cultivars, and provides additional evidence for the correlation between the genes and metabolites involved in flavonoid synthesis.

Oxidative stress is a major pathogenesis of some ocular surface diseases. Our previous study demonstrated that epidermal growth factor (EGF)-activated reactive oxygen species (ROS) could protect against human corneal epithelial cell (HCE) injury. In the present study, we aimed to explore the role and mechanisms of oxidative stress and mitochondrial autophagy in HCE cells subjected to scratch injury. CCK-8 assays, EdU assays, Western blot analysis, wound-healing assays, and flow cytometry were conducted to determine cell viability, proliferation, protein expression, cell apoptosis, and intracellular ROS levels, respectively. The results showed that EGF could promote damage repair and inhibit cell apoptosis in scratch injured HCE cells by upregulating ROS (**p < .01, ***p < .001). EGF also induced mitochondrial autophagy and alleviated mitochondrial damage. Interestingly, the combination of the mitochondrial autophagy inhibitor and mitochondrial division inhibitor 1 (MDIVI-1) with EGF could reduce cell proliferation, viability, and the ROS level (*p < .05, **p < .01, ***p < .001). Treatment using the ROS inhibitor N-acetyl- l-cysteine abrogated the increase in mitochondrial membrane potential after EGF treatment. (*p < .05). Taken together, these findings indicated that EGF plays an important role in HCE damage repair and could activate ROS to protect against HCE injury by inducing mitochondrial autophagy via activation of TRPM2.

The cell membranes of different cells deviate significantly in lipid compositions and thus provide varying biological environments to modulate the diffusion, organization and the resultant function of biomacromolecules. However, the detailed modulation mechanism remains elusive especially in consideration of the current overuse of the simplified membrane models such as the pure phosphatidylcholine (PC) membrane. In this work, with the typical membrane-active peptide melittin, we demonstrated that a more complicated membrane environment, such as the bacterial (IME) or plasma membrane (PM), would significantly change the organization and dynamics of melittin, by using molecular dynamics simulations as a "computational microscope". It was found that in these membrane systems, adding melittin would cause a varying degree of reduction in the lateral diffusion of lipids due to the different assembly states of peptides. Melittin tended to aggregate to oligomers in the pure PC membrane, mostly as a tetramer or trimer, while in IME or PM, its degree of oligomerization was significantly reduced. More surprisingly, melittin displayed a strong affinity with ganglioside GM3 in PM, leading to the formation of melittin-GM3 nanoclusters, which hindered its diffusion and further oligomerization. Additionally, small changes in the residue sequence of melittin could modulate the degree or structure of the peptide oligomer. Our work provides a typical example of a study on the organization and dynamics of pore-forming peptides in specific membrane environments and has great significance on the optimization of peptide sequences and the design of helix bundles in the membrane for target biological function.

Cytophaga hutchinsonii is a Gram-negative bacterium belonging to the phylum Bacteroidetes. It digests crystalline cellulose with an unknown mechanism and possesses a type IX secretion system (T9SS) that can recognize the C-terminal domain (CTD) of the cargo protein as a signal. In this study, the functions of the CTD in the secretion and localization of T9SS substrates in C. hutchinsonii were studied by fusing the green fluorescent protein (GFP) with the CTD from CHU_2708. The CTD is necessary for the secretion of GFP by C. hutchinsonii T9SS. The GFP-CTD(CHU_2708) fusion protein was found to be glycosylated in the periplasm, with a molecular mass about 5 kDa higher than that predicted from its sequence. The glycosylated protein was sensitive to peptide-N-glycosidase F, which can hydrolyze N-linked oligosaccharides. Analyses of mutants obtained by site-directed mutagenesis of asparagine residues in the N-X-S/T motif of CTD(CHU_2708) suggested that N-glycosylation occurred on the CTD. CTD N-glycosylation is important for the secretion and localization of GFP-CTD recombinant proteins in C. hutchinsonii. Glycosyltransferase-encoding gene chu_3842, a homologous gene of Campylobacter jejuni pglA, was found to participate in the N-glycosylation of C. hutchinsonii. Deletion of chu_3842 affected cell motility, cellulose degradation, and cell resistance to some chemicals. Our study provided evidence that the CTD as the signal of T9SS was N-glycosylated in the periplasm of C. hutchinsonii. IMPORTANCE The bacterial N-glycosylation system has previously been found only in several species of Proteobacteria and Campylobacterota, and the role of N-linked glycans in bacteria is still not fully understood. C. hutchinsonii has a unique cell contact cellulose degradation mechanism, and many cell surface proteins, including cellulases, are secreted by the T9SS. In this study, we found that C. hutchinsonii, a member of the phylum Bacteroidetes, has an N-glycosylation system. Glycosyltransferase CHU_3842 was found to participate in the N-glycosylation of C. hutchinsonii proteins and had effects on cell resistance to some chemicals, cell motility, and cellulose degradation. Moreover, N-glycosylation occurs on the CTD translocation signal of T9SS. The glycosylation of the CTD appears to play an important role in affecting T9SS substrate transportation and localization. This study enriched our understanding of the widespread existence and multiple biological roles of N-glycosylation in bacteria.

In new epidemics after the host shift, the pathogens may experience accelerated evolution driven by novel selective pressures. When the accelerated evolution enters a positive feedback loop with the expanding epidemics, the pathogen’s runaway evolution may be triggered. To test this possibility in COVID-19, we analyze the extensive databases and identify 5 major waves of strains, one replacing the previous one in 2020 – 2021. The mutations differ entirely between waves and the number of mutations continues to increase, from 3-4 to 21-31. The latest wave is the Delta strain which accrues 31 new mutations to become highly prevalent. Interestingly, these new mutations in Delta strain emerge in multiple stages with each stage driven by 6 – 12 coding mutations that form a fitness group. In short, the evolution of SARS-CoV-2 from the oldest to the youngest wave, and from the earlier to the later stages of the Delta wave, is a process of acceleration with more and more mutations. The global increase in the viral population size (M(t), at time t) and the mutation accumulation (R(t)) may have indeed triggered the runaway evolution in late 2020, leading to the highly evolved Alpha and then Delta strain. To suppress the pandemic, it is crucial to break the positive feedback loop between M(t) and R(t), neither of which has yet to be effectively dampened by late 2021. New waves beyond Delta, hence, should not be surprising.