RNA barcode segments for SARS-CoV-2 identification from HCoVs and SARSr-CoV-2 lineages.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for coronavirus disease 2019 (COVID-19), continues to evolve, giving rise to more variants and global reinfections. Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations. In this study, we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples, including human coronaviruses (HCoVs) and SARSr-CoV-2 lineages. Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets, encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages. Through genetic-level species testing, we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2. Subsequently, 75 main and subordinate species-specific barcode segments for SARS-CoV-2, located in ORF1ab, S, E, ORF7a, and N coding sequences, were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores. Post-testing, these segments exhibited high recall rates (nearly 100%), specificity (almost 30% at the nucleotide level), and precision (100%) performance on identification. They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database (http://virusbarcodedatabase.top/). The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis. Moreover, this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.

PNI, NLR and PLR combined detection prognosis of patients with chronic hepatitis C-associated cirrhosis complicated by T2DM.

INTRODUCTION: The prognostic nutrition index (PNI), neutrophil-to-lymphocyte ratio (NLR), and platelet-to-lymphocyte ratio (PLR) have been studied widely in the context of cancer; however, their correlation with chronic hepatitis C-associated cirrhosis complicated by type 2 diabetes mellitus (T2DM) is unknown. AIM: To investigate the correlation of the PNI, NLR, and PLR with chronic hepatitis C-associated cirrhosis complicated by T2DM. METHODOLOGY: We investigated 226 patients, comprising 56 patients with chronic hepatitis C-associated cirrhosis complicated by T2DM mellitus (group A), 85 patients with chronic hepatitis C-associated cirrhosis (group B), and 85 patients with T2DM (group C). The baseline data of all patients were analyzed. RESULTS: A comparison of baseline data among the three groups showed significant differences in age (p = 0.008). The levels of PNI were different among the three groups (p < 0.01). The NLR, PNI, and PLR were significantly different between the good and poor prognosis groups (p < 0.05). The AUC for the combined determination of PNI, NLR, and PLR, showed excellent diagnostic performance (AUC = 0.911, 95% CI 0.741-0.985, sensitivity = 80.00 %, and specificity = 88.89%). CONCLUSIONS: The PNI, NLR, and PLR were closely related to the prognosis of chronic hepatitis C-associated cirrhosis complicated by T2DM, and their combined detection had the highest specificity and sensitivity for the early prediction of the poor prognosis of chronic hepatitis C-associated cirrhosis complicated by T2DM, which has important clinical value.

NFIL3 aggravates human coronary artery endothelial cell injury by promoting ITGAM transcription in Kawasaki disease.

OBJECTIVE: High expression of nuclear factor interleukin-3 (NFIL3) and integrin Alpha M (ITGAM) was found in serum samples from Kawasaki disease (KD) patients through bioinformatics analysis. Hence, this study aimed to explore the biological functions of NFIL3 and ITGAM in KD serum-stimulated human coronary artery endothelial cells (HCAECs). METHODS: The differentially-expressed genes in KD were analyzed through bioinformatics analysis. Serum samples were obtained from 18 KD patients and 18 healthy volunteers, followed by detection of NFIL3 and ITGAM levels in KD serum. After HCAECs were transfected with sh-NFIL3, sh-ITGAM, or sh-NFIL3 + oe-ITGAM and underwent 24-h KD serum stimulation, cell viability and apoptosis and the levels of inflammation-related factors were measured. The binding between NFIL3 and ITGAM was validated by dual-luciferase and chromatin immunoprecipitation (ChIP) assays. RESULTS: NFIL3 and ITGAM were up-regulated in serum from KD patients and KD serum-stimulated HCAECs. Down-regulation of NFIL3 or ITGAM inhibited KD serum-induced cell apoptosis and inflammatory response of HCAECs and promoted cell viability. Mechanistically, NFIL3 promoted ITGAM transcription level. Up-regulation of ITGAM reversed the improvement of NFIL3 down-regulation on KD serum-induced HCAEC injury. CONCLUSION: NFIL3 aggravated KD serum-induced HCAEC injury by promoting ITGAM transcription, which provided new insights into the treatment of KD.

An in situ thermal cross-linking binder for silicon-based lithium ion battery.

Silicon has been regarded as one of the most promising anode materials for lithium-ion batteries (LIBs) due to its highest specific capacity and low (de)lithiation potential, however, the development of practical applications for silicon are still hindered by devastating volume expansion and low conductance. Herein, we have proposed an in situ thermally cross-linked water-soluble PA@PAA binder for silicon-based LIBs to construct dynamic cross-linking network. Specifically, ester bonds between -P-OH in phytic acid (PA) and -COOH in PAA, which are generated by thermal coupling, are designed to synergize with hydrogen bonds between the PA@PAA binder and silicon particles to dissipate the high mechanical stresses, which is verified by theoretical calculation. GO is further adopted to protect silicon particles from immediate contact with electrolyte to improve initial coulombic efficiency (ICE). A range of heat treatment temperatures is explored to optimize the previous process conditions and the optimum electrochemical performance is provided by Si@PA@PAA-220 electrodes with high reversible specific capacity of 1322.1 mAh/g at a current density of 0.5A/g after 510 cycles. Characterization has also revealed that PA@PAA is involved in electrochemical process and tunes the ratio of organic (LixPFy/LixPOyFZ)-inorganic (LiF) to consolidate solid electrolyte interface (SEI) during cycles. In brief, this applicable fascial in situ strategy can effectively improve the stability of silicon anodes for high energy density lithium-ion batteries.

Limimaricola litoreus sp. nov., isolated from intertidal sand of the Yellow Sea.

A novel species of the genus Limimaricola, designated ASW11-118T, was isolated from an intertidal sand sample of the Yellow Sea, PR China. Growth of strain ASW11-118T occurred at 10-40 °C (optimum, 28 °C), pH 5.5-8.5 (optimum, pH 7.5) and with 0.5-8.0 % (w/v) NaCl (optimum, 1.5%). Strain ASW11-118T has the highest 16S rRNA gene sequence similarity to Limimaricola cinnabarinus LL-001T (98.8%) and 98.6 % to Limimaricola hongkongensis DSM 17492T. Phylogenetic analysis based on genomic sequences indicated that strain ASW11-118T belongs to the genus Limimaricola. The genome size of strain ASW11-118T was 3.8 Mb and DNA G+C content was 67.8 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain ASW11-118T and other members of the genus Limimaricola were below 86.6 and 31.3 %, respectively. The predominant respiratory quinone was ubiquinone-10. The predominant cellular fatty acid was C18 : 1 ω7c. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and one unknown aminolipid. On the basis of the data presented, strain ASW11-118T is considered to represent a novel species of the genus Limimaricola, for which the name Limimaricola litoreus sp. nov. is proposed. The type strain is ASW11-118T (=MCCC 1K05581T=KCTC 82494T).

Rationally designed rGO@CNTs@CNFs film as self-supporting binder-free Si electrodes for high-performance lithium-ion batteries.

Si has become the most promising anode materials for lithium-ion batteries (LIBs) due to its high theoretical specific capacity and comparable low discharge potential. However, the practical usage of Si is still hindered by its huge volume expansion. To release volume stress and improve conductance, designed self-supporting binder-free Si electrode endowed with three-dimensional structure has been come up in this research. The pore structure is adjusted by rationally designing the proportion of carbon nanotubes (CNTs) and carbon nanofibers (CNFs) to alleviate volume change. Simultaneously, construct stable conductivity network was fabricated via ice crystal self-assemble freezing technique following compress and carbonization process. The electrochemical specific capacity of rGO@CNTs@CNFs@Si-2 electrode has stably remained at 2250 mAh/g after 100 cycles (100 mA/g) with benign rate capabilities. This simple self-assemble method for self-supporting binder-free Si electrode would open a new route to exploit high energy density Si-based electrode for flexible LIBs.

Group velocity dispersion in high-performance BH InAs/InP QD and InGaAsP/InP QW two-section passively mode-locked lasers.

High-performance buried heterostructure (BH) C-band InAs/InP quantum dot (QD) and L-band InGaAsP/InP quantum well (QW) two-section passively mode-locked lasers (MLLs) are investigated. From the irregularity of the longitudinal mode spacing in the comb spectra, we confirm that under stable passive mode locking, both devices have strong group velocity dispersion (GVD) and corresponding GVD-induced pulse width broadening. After compensation with anomalous dispersion fibers (SMF-28), short pulse trains with sub-ps pulse widths are achieved for both devices. This observation demonstrates our ability to generate high peak power sub-ps pulses using QD MLLs and QW MLLs for many photonic applications of optical communications.

ABHD16A Negatively Regulates the Palmitoylation and Antiviral Function of IFITM Proteins.

Interferon-inducible transmembrane (IFITM) proteins are small homologous proteins that are encoded by the interferon-stimulated genes (ISGs), which can be strongly induced by interferon (IFN) and provide resistance to invasion by a variety of viral pathogens. However, the exact molecular mechanisms underlying this function have remained elusive. The antiviral activity of IFITMs from different species depends on S-palmitoylation at conserved cysteine residues. However, specific enzymes involved in the dynamic palmitoylation cycle of IFITMs, especially depalmitoylase, have not yet been reported. Here, we demonstrate that α/-hydrolase domain-containing 16A (ABHD16A) is a depalmitoylase and a negative regulator of IFITM protein that can catalyze the depalmitoyl reaction of S-palmitoylated IFITM proteins, thereby decreasing their antiviral activities on RNA viruses. Using the acyl-PEGyl exchange gel shift (APEGS) assay, we identified ABHD16A proteins from humans, pigs, and mice that can directly participate in the palmitoylation/depalmitoylation cycles of IFITMs in the constructed abhd16a-/- cells and ABHD16A-overexpressing cells. Furthermore, we showed that ABHD16A functions as a regulator of subcellular localization of IFITM proteins and is related to the immune system. It is tempting to suggest that pharmacological intervention in IFITMs and ABHD16A can be achieved either through controlling their expression or regulating their activity, thereby providing a broad-spectrum therapeutic strategy for animal viral diseases. IMPORTANCE IFITM protein is the cells first line of antiviral defense that blocks early stages of viral replication; the underlying mechanism might be associated with the proper distribution in cells. The palmitoylation/depalmitoylation cycle can dynamically regulate protein localization, stability, and function. This work is the first one that found the critical enzyme that participates in the palmitoylation/depalmitoylation cycle of IFITM, and this type of palmitoyl loss may be an essential regulation mode for balancing the antiviral functions of the IFN pathway. These findings imply that the pharmacological intervention in IFITM and ABHD16A, either through controlling their expression or regulating their activities, could provide a broad-spectrum therapeutic strategy for animal viral diseases and complications linked to interferon elevation.

Celeribacter litoreus sp. nov., isolated from intertidal sediment.

A Gram-negative, aerobic, non-flagellated and rod-shaped bacterium, strain ASW11-22T, was isolated from an intertidal sediment collected from a coastal area of Qingdao, PR China. The strain grew at 15-40 °C (optimum, 37 °C), at pH 6.0-9.0 (optimum, pH 7.0) and with 0.5-10 % (w/v) NaCl (optimum, 1.0 %). It hydrolysed gelatin and aesculin but did not reduce nitrate to nitrite. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ASW11-22T belonged to the genus Celeribacter, showing the highest sequence similarity to the type strains of Celeribacter halophilus MCCC 1A06432T (98.20 %) and Celeribacter ethanolicus NH195T (97.84 %). The genomic DNA G+C content was 59.1 mol%. The major cellular fatty acid (>10 %) of the strain was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and its main polar lipids were phosphatidylglycerol and one unidentified aminolipid. The sole respiratory quinone of strain ASW11-22T was ubiquinone-10. On the basis of the polyphasic evidence presented in this paper, strain ASW11-22T represents a novel Celeribacter species, for which the name Celeribacter litoreus sp. nov. is proposed. The type strain is ASW11-22T (=KCTC 82495T=MCCC 1K05584T).

Validation of QTLs for Fiber Quality Introgressed from Gossypium mustelinum by Selective Genotyping.

Gene introgression from wild species has been shown to be a feasible approach for fiber quality improvement in Upland cotton. Previously, we developed an interspecific G. mustelinum × G. hirsutum advanced-backcross population and mapped over one hundred QTL for fiber quality traits. In the current study, a trait-based selective genotyping approach was utilized to prioritize a small subset of introgression lines with high phenotypic values for different fiber quality traits, to simultaneously validate multiple fiber quality QTL in a single experiment. A total of 75 QTL were detected by CIM and/or single-marker analysis, including 11 significant marker-trait associations (P < 0.001) and three putative associations (P < 0.005) also reported in earlier studies. The QTL that have been validated include three each for fiber length, micronaire, and elongation, and one each for fiber strength and uniformity. Collectively, about 10% of the QTL previously reported have been validated here, indicating that selective genotyping has the potential to validate multiple marker-trait associations for different traits, especially those with a moderate to large-effect detected simultaneously in one experimental population. The G. mustelinum alleles contributed to improved fiber quality for all validated loci. The results from this study will lay the foundation for further fine mapping, marker-assisted selection and map-based gene cloning.

Single longitudinal mode GaAs-based quantum dot laser with refractive index perturbation.

We report on the design, fabrication, and characterization of single longitudinal mode InAs/GaAs quantum dot lasers emitting at the 1.3 µm communication band. The influence of simply etched surface high-order gratings in the ridge of the Fabry-Perot lasers has been studied. A 35th-order surface grating is fabricated by standard photolithography to introduce the refractive index perturbation, which leads to the reduced mirror loss at the desired wavelength and thus realizing single longitudinal mode lasing. Stable single-mode operations are maintained at the injection current range of 45-100 mA with a side-mode suppression ratio up to 33 dB.

Cytotoxic and anti-inflammatory activities of phenanthrenes from the medullae of Juncus effusus L.

Bioactivity guided phytochemical investigation of the ethanol extract of the medullae of Juncus effusus resulted in the isolation of two new phenanthrenes, 8-hydroxymethyl-2-hydroxyl-1-methyl-5-vinyl-9,10-dihydrophenanthrene (1), and 5-(1-methoxyethyl)-1-methyl-phenanthren-2,7-diol (2) together with 15 known phenanthrenoids (3-17). The chemical structures of 1 and 2 were established by a combination of spectroscopic techniques. Compounds 1-15 and 17 were evaluated for their cytotoxic activities against five human cancer cell lines (SHSY-5Y, SMMC-7721, HepG-2, Hela and MCF-7) by CCK-8 assay, and their anti-inflammatory activities were also evaluated by inhibition on NO production in LPS-activated murine macrophage RAW 264.7 cells.

[Chemical constituents from Phellinus igniarius and their anti-tumor activity in vitro].

Eleven compounds were isolated and purified from Phellinus igniarius by column chromatography on silica gel, Sephedax LH-20, RP-8, MCI and preparative TLC. Their structures were identified as 3α-hydroxyfriedel-2-one (1), 3-hydroxyfriedel-3-en-2-one (2), ergosta-4, 6, 8 (14), 22-tetraen-3-one (3), ergosterol peroxide (4), uracil (5), uridine (6), 4-(3, 4-dihydroxyphenyl)-3-butene-2-one (7), protocatechualdehyde (8), inotilone (9), inoscavinA (10) and phellibaumin E (11), respectively, on the basis of NMR and MS data analysis. Among them, compounds 1, 2, 5, and 6 were firstly obtained from this genus. In vitro cytotoxic activity of compounds 1-11 was screened by Cell Titer-GLo Reagent, on 41 human tumor cell strains and 2 hamster normal cell strains via high-throughput screening. Compounds 2-4 exhibit significant cytotoxic activity against NOMO-1 and SKM-1 acute myeloid leukemia cell lines, and compounds 2 and 3 showed good selectivity to NOMO-1 with IC50 values of 0.795 5, 1.828 µmol•L-1and SKM-1 with IC50 values of higher than 10 µmol•L-1. Compound 7 showed remarkable antitumor activities against H526 Human lung cancer cell line, DU145 prostate cancer cell line and HEL erythroleukemia cell line with IC50 values of 0.533 4, 1.885, 1.057 µmol•L⁻¹, respectively. Other compounds had no or weak antitumor effect. In addition, all compounds had no significant effect on hamster normal cell lines CHL and CHO with IC50 values of higher than 10 µmol•L⁻¹, which showed that all compounds had no toxic effect on normal cells.

Four new phenanthrenoid dimers from Juncus effusus L. with cytotoxic and anti-inflammatory activities.

Four new phenanthrenoid dimers, effususins A-D (1-4), were isolated from an ethanolic extract of the medullae of Juncus effuses (Juncaceae). Their structures were elucidated by 1D and 2D NMR spectroscopic analysis and mass spectrometry. Compounds 1-4 was in vitro evaluated for their cytotoxic activities by CCK-8 assay against five human cancer cell lines (SHSY-5Y, SMMC-7721, HepG2, Hela, and MCF-7) and their inhibitory effects on NO production in lipopolysaccharide-activated murine macrophage RAW264.7 cells. Effususin B exhibited moderate to strong cytotoxic activities against the tested cancer cell lines and moderate anti-inflammatory activity.