Transcriptome analysis of the harmful alga Heterosigma akashiwo under a 24-hour light-dark cycle.

The photoperiod, which is defined as the period of time within a 24-hour time frame that light is available, is an important environmental regulator of several physiological processes in phytoplankton, including harmful bloom-forming phytoplankton. The ichthyotoxic raphidophyte Heterosigma akashiwo is a globally distributed bloom-forming phytoplankton. Despite extensive studies on the ecological impact of H. akashiwo, the influence of the photoperiod on crucial biological processes of this species remains unclear. In this study, gene expression in H. akashiwo was analyzed over a 24-hour light-dark (14:10) treatment period. Approximately 36 % of unigenes in H. akashiwo were differentially expressed during this 24-hour treatment period, which is indicative of their involvement in the response to light-dark variation. Notably, the number of differentially expressed genes exhibited an initial increase followed by a subsequent decrease as the sampling time progressed (T0 vs. other time points). Unigenes associated with photosynthesis and photoprotection reached their peak expression levels after 2-4 h of illumination (T12-T14). In contrast, the expression of unigenes associated with DNA replication peaked at the starting point of the dark period (T0). Furthermore, although several unigenes annotated to photoreceptors displayed potential diel periodicity, genes from various photoreceptor families (such as phytochrome and cryptochrome) showed unique expression patterns. Collectively, our findings offer novel perspectives on the response of H. akashiwo to the light-dark cycle, serving as a valuable resource for investigating the physiology and ecology of this species.

Preservation of the pulmonary branches of the vagus nerve during three-dimensional thoracoscopic radical resection of lung cancer: a retrospective study.

BACKGROUND: In this study, we investigated the effect of preservation of the pulmonary branches of the vagus nerve during systematic dissection of mediastinal lymph nodes, when performing radical resection of lung cancer, on the postoperative complication rate. METHODS: The clinical data for 80 patients who underwent three-dimensional thoracoscopic radical resection of lung cancer in the Department of Thoracic Surgery at Huizhou Municipal Central Hospital between 2020 and 2022 were analyzed. The patients were divided into two groups according to whether the pulmonary branches of the vagus nerve were retained during intraoperative carinal lymph node dissection. The operation time, time until first postoperative defecation, duration for which a chest tube was needed, total chest drainage volume, average pain intensity during the first 5 postoperative days, incidence of postoperative pneumonia, and postoperative length of stay were compared between the two groups. RESULTS: There was no statistically significant difference in histological staging or in time until first postoperative defecation between the two groups (p > 0.05). However, there were significant differences in operation time, the duration for which a chest tube was needed, total chest drainage volume, average pain intensity during the first 5 postoperative days, white blood cell count and procalcitonin level on postoperative days 1 and 5, and postoperative length of stay between the two groups (p < 0.05). CONCLUSION: Preserving the pulmonary branches of the vagus nerve during carinal lymph node dissection when performing three-dimensional thoracoscopic radical resection of lung cancer can reduce the risk of postoperative complications.

A face image classification method of autistic children based on the two-phase transfer learning.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder, which seriously affects children's normal life. Screening potential autistic children before professional diagnose is helpful to early detection and early intervention. Autistic children have some different facial features from non-autistic children, so the potential autistic children can be screened by taking children's facial images and analyzing them with a mobile phone. The area under curve (AUC) is a more robust metrics than accuracy in evaluating the performance of a model used to carry out the two-category classification, and the AUC of the deep learning model suitable for the mobile terminal in the existing research can be further improved. Moreover, the size of an input image is large, which is not fit for a mobile phone. A deep transfer learning method is proposed in this research, which can use images with smaller size and improve the AUC of existing studies. The proposed transfer method uses the two-phase transfer learning mode and the multi-classifier integration mode. For MobileNetV2 and MobileNetV3-Large that are suitable for a mobile phone, the two-phase transfer learning mode is used to improve their classification performance, and then the multi-classifier integration mode is used to integrate them to further improve the classification performance. A multi-classifier integrating calculation method is also proposed to calculate the final classification results according to the classifying results of the participating models. The experimental results show that compared with the one-phase transfer learning, the two-phase transfer learning can significantly improve the classification performance of MobileNetV2 and MobileNetV3-Large, and the classification performance of the integrated classifier is better than that of any participating classifiers. The accuracy of the integrated classifier in this research is 90.5%, and the AUC is 96.32%, which is 3.51% greater than the AUC (92.81%) of the previous studies.

Isolation and Genomics of Futiania mangrovii gen. nov., sp. nov., a Rare and Metabolically Versatile Member in the Class Alphaproteobacteria.

Mangrove microorganisms are a major part of the coastal ecosystem and are directly associated with nutrient cycling. Despite their ecological significance, the collection of culturable mangrove microbes is limited due to difficulties in isolation and cultivation. Here, we report the isolation and genome sequence of strain FT118T, the first cultured representative of a previously uncultivated order UBA8317 within Alphaproteobacteria, based on the combined results of 16S rRNA gene similarity, phylogenomic, and average amino acid identity analyses. We propose Futianiales ord. nov. and Futianiaceae fam. nov. with Futiania as the type genus, and FT118T represents the type species with the name Futiania mangrovii gen. nov, sp. nov. The 16S rRNA gene sequence comparison reveals that this novel order is a rare member but has a ubiquitous distribution across various habitats worldwide, which is corroborated by the experimental confirmation that this isolate can physiologically adapt to a wide range of oxygen levels, temperatures, pH and salinity levels. Biochemical characterization, genomic annotation, and metatranscriptomic analysis of FT118T demonstrate that it is metabolically versatile and active in situ. Genomic analysis reveals adaptive features of Futianiales to fluctuating mangrove environments, including the presence of high- and low-affinity terminal oxidases, N-type ATPase, and the genomic capability of producing various compatible solutes and polyhydroxybutyrate, which possibly allow for the persistence of this novel order across various habitats. Collectively, these results expand the current culture collection of mangrove microorganisms, providing genomic insights of how this novel taxon adapts to fluctuating environments and the culture reference to unravel possible microbe-environment interactions. IMPORTANCE The rare biosphere constitutes an essential part of the microbial community and may drive nutrient cycling and other geochemical processes. However, the difficulty in microbial isolation and cultivation has hampered our understanding of the physiology and ecology of uncultured rare lineages. In this study, we successfully isolated a novel alphaproteobacterium, designated as FT118T, and performed a combination of phenotypic, phylogenetic, and phylogenomic analyses, confirming that this isolate represents the first cultured member of a previously uncultivated order UBA8317 within Alphaproteobacteria. It is a rare species with a ubiquitous distribution across different habitats. Genomic and metatranscriptomic analyses demonstrate that it is metabolically versatile and active in situ, suggesting its potential role in nutrient cycling despite being scarce. This work not only expands the current phylogeny of isolated Alphaproteobacteria but also provides genomic and culture reference to unravel microbial adaptation strategies in mangrove sediments and possible microbe-environment interactions.

Circ_0010235 facilitates lung cancer development and immune escape by regulating miR-636/PDL1 axis.

BACKGROUND: Circular RNAs (circRNAs) are a class of important regulators in various human cancers, including lung cancer. Here, we aimed to investigate the role of circ_0010235 in lung cancer. METHODS: The expression of circ_0010235, microRNA-636 (miR-636) and PDL1 was measured by quantitative real-time PCR (qRT-PCR). Cell proliferation was evaluated by CCK-8, colony formation, and 5-ethynyl-2'-deoxyuridine (EdU) assays. Cell apoptosis was detected by flow cytometry. Cell invasion was assessed by transwell assay. All protein levels were determined by western blot assay. In order to detect the roles of circ_0010235 in immune escape, lung cancer cells were cocultured with peripheral blood mononuclear cells (PBMCs) or cytokine-induced killer (CIK) cells in vitro. The relationship between miR-636 and circ_0010235 or PDL1 was verified by dual-luciferase reporter assay and RNA pulldown assay. Immunohistochemistry (IHC) analysis was used to detect Ki67 and programmed death-ligand 1 (PDL1) expression. A xenograft tumor model was established to verify the function of circ_0010235 in vivo. RESULTS: Circ_0010235 was overexpressed in lung cancer. Circ_0010235 knockdown inhibited proliferation, invasion and immune escape and promoted apoptosis of lung cancer cells. MiR-636 was a target of circ_0010235, and miR-636 inhibition reversed the effects of circ_0010235 knockdown in lung cancer cells. PDL1 was a direct target of miR-636, and miR-636 suppressed the proliferation and invasion and increased apoptosis and antitumor immunity in lung cancer cells by downregulating PDL1. Moreover, circ_0010235 positively regulated PDL1 expression by sponging miR-636. Additionally, circ_0010235 knockdown hampered tumorigenesis in vivo. CONCLUSION: Circ_0010235 knockdown inhibited lung cancer progression and increased antitumor immunity by regulating the miR-636/PDL1 axis.

Comparative genomic analysis reveals metabolic flexibility of Woesearchaeota.

The archaeal phylum Woesearchaeota, within the DPANN superphylum, includes phylogenetically diverse microorganisms that inhabit various environments. Their biology is poorly understood due to the lack of cultured isolates. Here, we analyze datasets of Woesearchaeota 16S rRNA gene sequences and metagenome-assembled genomes to infer global distribution patterns, ecological preferences and metabolic capabilities. Phylogenomic analyses indicate that the phylum can be classified into ten subgroups, termed A-J. While a symbiotic lifestyle is predicted for most, some members of subgroup J might be host-independent. The genomes of several Woesearchaeota, including subgroup J, encode putative [FeFe] hydrogenases (known to be important for fermentation in other organisms), suggesting that these archaea might be anaerobic fermentative heterotrophs.

Single-port VATS combined with non-indwelling drain in ERAS: a retrospective study.

BACKGROUND: We investigated single-port video-assisted thoracoscopic surgery (VATS) combined with a postoperative non-indwelling drain in enhanced recovery after surgery (ERAS). METHODS: The clinical data of 127 patients who underwent double- and single-port VATS from January 2018 to December 2019 were analyzed retrospectively. The groups constituted 71 cases undergoing double-port and 56 cases undergoing single-port VATS (30 cases in the indwelling drain group and 26 cases in the non-indwelling drain group). The incidence of postoperative complications, pain scores, and postoperative hospital stay were compared between the two groups. RESULTS: Compared with the double-port group, the single-port group had shorter postoperative hospital stays and lower pain scores on the first and third postoperative days (P < 0.05). Pain scores on the first and third days were lower in the single-port non-indwelling drain group than in the single-port indwelling drain group (P < 0.05), and the postoperative hospitalization time was significantly shorter in the single-port group (P < 0.05). However, there was no significant difference between the two groups for operation time, incidence of complications, and pain scores 1 month after operation (P > 0.05). CONCLUSIONS: The combination of single-port VATS with a non-indwelling drain can relieve postoperative pain, help patients recover quickly, and is in accordance with ERAS.

Expanded diversity of Asgard archaea and their relationships with eukaryotes.

Asgard is a recently discovered superphylum of archaea that appears to include the closest archaeal relatives of eukaryotes1-5. Debate continues as to whether the archaeal ancestor of eukaryotes belongs within the Asgard superphylum or whether this ancestor is a sister group to all other archaea (that is, a two-domain versus a three-domain tree of life)6-8. Here we present a comparative analysis of 162 complete or nearly complete genomes of Asgard archaea, including 75 metagenome-assembled genomes that-to our knowledge-have not previously been reported. Our results substantially expand the phylogenetic diversity of Asgard and lead us to propose six additional phyla that include a deep branch that we have provisionally named Wukongarchaeota. Our phylogenomic analysis does not resolve unequivocally the evolutionary relationship between eukaryotes and Asgard archaea, but instead-depending on the choice of species and conserved genes used to build the phylogeny-supports either the origin of eukaryotes from within Asgard (as a sister group to the expanded Heimdallarchaeota-Wukongarchaeota branch) or a deeper branch for the eukaryote ancestor within archaea. Our comprehensive protein domain analysis using the 162 Asgard genomes results in a major expansion of the set of eukaryotic signature proteins. The Asgard eukaryotic signature proteins show variable phyletic distributions and domain architectures, which is suggestive of dynamic evolution through horizontal gene transfer, gene loss, gene duplication and domain shuffling. The phylogenomics of the Asgard archaea points to the accumulation of the components of the mobile archaeal 'eukaryome' in the archaeal ancestor of eukaryotes (within or outside Asgard) through extensive horizontal gene transfer.

Ecological features and global distribution of Asgard archaea.

Asgard is a newly proposed archaeal superphylum, which has been suggested to hold the key to decipher the origin of Eukaryotes. However, their ecology remains largely unknown. Here, we conducted a meta-analysis of publicly available Asgard-associated 16S rRNA gene fragments, and found that just three previously proposed clades (Lokiarchaeota, Thorarchaeota, and Asgard clade 4) are widely distributed, whereas the other seven clades (phylum or class level) are restricted to the sediment biosphere. Asgard archaea, especially Loki- and Thorarchaeota, seem to adapt to marine sediments, and water depth (the depth of the sediment below water surface) and salinity might be crucial factors for the proportion of these microorganisms as revealed by multivariate regression analyses. However, the abundance of Asgard archaea exhibited distinct environmental drivers at the clade-level; for instance, the proportion of Asgard clade 4 was higher in less saline environments (salinity <6.35 psu), while higher for Heimdallarchaeota-AAG and Asgard clade 2 in more saline environment (salinity ≥35 psu). Furthermore, co-occurrence analysis allowed us to find a significant non-random association of different Asgard clades with other groups (e.g., Lokiarchaeota with Deltaproteobacteria and Anaerolineae; Odinarchaeota with Bathyarchaeota), suggesting different interaction potentials among these clades. Overall, these findings reveal Asgard archaea as a ubiquitous group worldwide and provide initial insights into their ecological features on a global scale.

Comparative genomic analysis reveals metabolic diversity of different Paenibacillus groups.

The genus Paenibacillus was originally recognized based on the 16S rRNA gene phylogeny. Recently, a standardized bacterial taxonomy approach based on a genome phylogeny has substantially revised the classification of Paenibacillus, dividing it into 23 genera. However, the metabolic differences among these groups remain undescribed. Here, genomes of 41 Paenibacillus strains comprising 25 species were sequenced, and a comparative genomic analysis was performed considering these and 187 publicly available Paenibacillus genomes to understand their phylogeny and metabolic differences. Phylogenetic analysis indicated that Paenibacillus clustered into 10 subgroups. Core genome and pan-genome analyses revealed similar functional categories among the different Paenibacillus subgroups; however, each group tended to harbor specific gene families. A large proportion of genes in the subgroups A, E, and G are related to carbohydrate metabolism. Among them, genes related to the glycoside hydrolase family were most abundant. Metabolic reconstruction of the newly sequenced genomes showed that the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, and citric acid cycle are central pathways of carbohydrate metabolism in Paenibacillus. Further, the genomes of the subgroups A and G lack genes involved in glyoxylate cycle and D-galacturonate degradation, respectively. The current study revealed the metabolic diversity of Paenibacillus subgroups assigned based on a genomic phylogeny and could inform the taxonomy of Paenibacillus. KEY POINTS: • Paenibacillus clustered into 10 subgroups. • Genomic content variation and metabolic diversity in the subgroup A, E, and G were described. • Carbohydrate transport and metabolism is important for Paenibacillus survival.

[Advances in microbial degradation of polybrominated diphenyl ethers (PBDEs)].

Polybrominated diphenyl ethers (PBDEs) are widely used brominated flame-retardants in a variety of commercial products especially in the electronics and household industries. However, they are bioaccumulative, biotoxic and persistent, making them a globally distributed organic chemical toxin nowadays. Thus, it is extremely important to degrade PBDEs. This paper illustrates the research progress of metabolic pathways of PBDEs under both aerobic and anaerobic conditions, and also combines with in situ degradation studies to infer the degradation potential of archaea. The characteristics and comprehensive factors of various degradation pathways are analyzed. In addition, future researches on biodegradation mechanism of PBDEs, the design and application of PBDEs degradation system are discussed.

Dynamics of microbial community in the bioreactor for bisphenol S removal.

Bisphenol S is one of the alternative substitutes of Bisphenol A, a chemical widely recognized as an endocrine disrupting compound. In the past few years, a variety of studies on degradation of BPA demonstrated that microorganisms play important roles in the degradation process. However, the fate of BPS during wastewater treatment processes and the composition of microorganisms that functionalize BPS degradation remain to be explored. In this study, three bioreactors, R-BPS (amended with Bisphenol S), R-BPSHA (amended with Bisphenol S and humic acid) and Con (control bioreactor), were set up to investigate the fate of BPS and the microbial compositions and dynamics in the bioreactors, especially for the microorganisms associated with BPS removal. Results showed that a complete removal was achieved within 24 days. The addition of humic acid accelerated the elimination of BPS in both effluent and sludge. The results of 16S rRNA gene ampilicon sequencing revealed that the most abundant bacteria in all samples were affiliated to Proteobacteria, Bacteroidetes, Acidobacteria and Chloroflexi. Seven major genera were likely associated with BPS removal, including Pseudomonas, Azospira, Hydrogenophaga, Devosia, Delftia, Acidovorax and Rhodobacter. Among them, humic acid increased relative abundance of some bacteria, such as Pseudomonas, Hydrogenophaga and Acidovorax. These findings would give valuable information on the microbial community composition associated with BPS removal, providing biological background for bioremediation of BPS-contaminated environment.

Bottom-Up and Top-Down Approaches to Explore Sodium Dodecyl Sulfate and Soluplus on the Crystallization Inhibition and Dissolution of Felodipine Extrudates.

The objectives of this study were to explore sodium dodecyl sulfate (SDS) and Soluplus on the crystallization inhibition and dissolution of felodipine (FLDP) extrudates by bottom-up and top-down approaches. FLDP extrudates with Soluplus and SDS were prepared by hot melt extrusion, and characterized by polarized light microscopy, differential scanning calorimetry, and fourier transform infrared spectroscopy. Results indicated that Soluplus inhibited FLDP crystallization, and the whole amorphous solid dispersions (ASDs) were binary FLDP-Soluplus (1:3) and ternary FLDP-Soluplus-SDS (1:2:0.15∼0.3 and 1:3:0.2∼0.4) extrudates. Internal SDS (5%-10%) decreased glass transition temperatures of FLDP-Soluplus-SDS ternary ASDs without presenting molecular interactions with FLDP or Soluplus. The enhanced dissolution rate of binary or ternary Soluplus-rich ASDs in the nonsink condition of 0.05% SDS was achieved. Bottom-up approach indicated that Soluplus was a much stronger crystal inhibitor to the supersaturated FLDP in solutions than SDS. Top-down approach demonstrated that SDS enhanced the dissolution of Soluplus-rich ASDs via wettability and complexation with Soluplus to accelerate the medium uptake and erosion kinetics of extrudates, but induced FLDP recrystallization and resulted in incomplete dissolution of FLDP-rich extrudates. In conclusion, top-down approach is a promising strategy to explore the mechanisms of ASDs' dissolution, and small amount of SDS enhances the dissolution rate of polymer-rich ASDs in the nonsink condition.

The Synergetic Effects of Nonpolar and Polar Protic Solvents on the Properties of Felodipine and Soluplus in Solutions, Casting Films, and Spray-Dried Solid Dispersions.

The aim was to explore the effects of nonpolar and polar protic solvents composed of dichloromethane (DCM) and ethanol (EtOH) on the properties of felodipine (FLDP) and Soluplus in solutions, casting films, and spray-dried drug-rich or polymer-rich solid dispersions (SDs). Measurement of intrinsic viscosity and solubility indicated that FLDP and Soluplus were miscible. EtOH-DCM ranging from 20:80 to 50:50 induced the strongest molecular interactions for FLDP-Soluplus-solvents systems. Accordingly, the casting films and spray-dried powders of FLDP and Soluplus were prepared using pure EtOH or DCM and their mixtures as solvents. Polarized light microscopy, differential scanning calorimetry, Fourier transform infrared spectroscopy, in vitro dissolution tests, and stability have been conducted to characterize these films or spray-dried powders. EtOH-DCM (50:50) showed δH 2-3 MPa1/2 higher than FLDP and Soluplus. It exhibited stronger inhibitory effects on phase separation and recrystallization of amorphous FLDP than pure DCM or EtOH in the drug-rich casting films, spray drying process, and spray-dried SDs exposure to 40°C/RH75% for 1 month. Higher ratio of Soluplus may offset the effects of solvents on the dissolution and stability of polymer-rich SDs. In conclusion, combination of nonpolar and polar protic solvents is of high potential for spray drying to optimize drug-rich SDs.

Novel self-assembled tacrolimus nanoparticles cross-linking thermosensitive hydrogels for local rheumatoid arthritis therapy.

The aim was to explore the potential application of novel self-assembled nanoparticles cross-linking thermosensitive hydrogels composed of polyvinyl caprolactam-polyvinyl acetate-polyethylene glycol (Soluplus) and tacrolimus (FK-506) for local therapy of rheumatoid arthritis (RA). The sol-gel transition temperature (Tsol-gel), gelation time, rheological behaviors, in vitro release, in vivo gelation and retention, and therapeutic efficacy against adjuvant-induced arthritis (AIA) rats were compared between the Soluplus hydrogels and widely studied poloxamer 407 (P407) delivery systems. In sol, the spherical and uniform FK506 loaded Soluplus nanoparticles (Soluplus-SNPs) were self-assembled with encapsulation efficiency of 99.5±1.5% and particle size of 73.9±2.9nm. The decreased Tsol-gel of Soluplus-SNPs hydrogels was associated with the addition of salts, elevation of pH and ionic strength. The optimal Tsol-gel of Soluplus-SNPs with concentrations of 10%-30% in phosphate buffer (50mM, pH 7.4) was from 37.4±0.1°C to 32.8±0.3°C and the gelation time was not greater than 2min. Soluplus-SNPs gelling systems showed lower viscosity and wider range concentrations in sol state at 25°C and stronger gel strength at 37°C than P407, which resulting in longer sustained release of FK506 but without burst-release in vitro, and longer retention time in the local injection site in vivo. The therapeutic efficacy to treat AIA rats was significantly enhanced from d10 to d17 after a single dose of FK506 loaded in 10% and 20% Soluplus-SNPs hydrogels. In conclusion, Soluplus-SNPs hydrogel is a potential sustainable delivery system for FK506 to treat RA locally.