Metatranscriptome of human lung microbial communities in a cohort of mechanically ventilated COVID-19 Omicron patients.

The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) infected a substantial proportion of Chinese population, and understanding the factors underlying the severity of the disease and fatality is valuable for future prevention and clinical treatment. We recruited 64 patients with invasive ventilation for COVID-19 and performed metatranscriptomic sequencing to profile host transcriptomic profiles, plus viral, bacterial, and fungal content, as well as virulence factors and examined their relationships to 28-day mortality were examined. In addition, the bronchoalveolar lavage fluid (BALF) samples from invasive ventilated hospital/community-acquired pneumonia patients (HAP/CAP) sampled in 2019 were included for comparison. Genomic analysis revealed that all Omicron strains belong to BA.5 and BF.7 sub-lineages, with no difference in 28-day mortality between them. Compared to HAP/CAP cohort, invasive ventilated COVID-19 patients have distinct host transcriptomic and microbial signatures in the lower respiratory tract; and in the COVID-19 non-survivors, we found significantly lower gene expressions in pathways related viral processes and positive regulation of protein localization to plasma membrane, higher abundance of opportunistic pathogens including bacterial Alloprevotella, Caulobacter, Escherichia-Shigella, Ralstonia and fungal Aspergillus sydowii and Penicillium rubens. Correlational analysis further revealed significant associations between host immune responses and microbial compositions, besides synergy within viral, bacterial, and fungal pathogens. Our study presents the relationships of lower respiratory tract microbiome and transcriptome in invasive ventilated COVID-19 patients, providing the basis for future clinical treatment and reduction of fatality.

PD-1 inhibitor plus anlotinib for metastatic castration-resistant prostate cancer: a real-world study.

Management and treatment of terminal metastatic castration-resistant prostate cancer (mCRPC) remains heavily debated. We sought to investigate the efficacy of programmed cell death 1 (PD-1) inhibitor plus anlotinib as a potential solution for terminal mCRPC and further evaluate the association of genomic characteristics with efficacy outcomes. We conducted a retrospective real-world study of 25 mCRPC patients who received PD-1 inhibitor plus anlotinib after the progression to standard treatments. The clinical information was extracted from the electronic medical records and 22 patients had targeted circulating tumor DNA (ctDNA) next-generation sequencing. Statistical analysis showed that 6 (24.0%) patients experienced prostate-specific antigen (PSA) response and 11 (44.0%) patients experienced PSA reduction. The relationship between ctDNA findings and outcomes was also analyzed. DNA-damage repair (DDR) pathways and homologous recombination repair (HRR) pathway defects indicated a comparatively longer PSA-progression-free survival (PSA-PFS; 2.5 months vs 1.2 months, P = 0.027; 3.3 months vs 1.2 months, P = 0.017; respectively). This study introduces the PD-1 inhibitor plus anlotinib as a late-line therapeutic strategy for terminal mCRPC. PD-1 inhibitor plus anlotinib may be a new treatment choice for terminal mCRPC patients with DDR or HRR pathway defects and requires further investigation.

Soluble expression, rapid purification, biological identification of chicken interferon-alpha using a thioredoxin fusion system in E. coli and its antiviral effects to H9N2 avian influenza virus.

In this paper, we report a soluble expression based on Escherichia coli and two-step purification of a novel thioredoxin-tagged chicken interferon-α fusion protein (Trx-rChIFN-α) by using pET32a(+) expression system. The mature ChIFN-α gene was amplified by Reverse transcriptase-polymerase chain reaction (RT-PCR) and subcloned into pET-32a (+) vector prior to transformation into Rosetta (DE3) competent cells. After IPTG induction, the recombinant fusion protein was expressed efficiently in the soluble fraction. The protein purification was performed by nickel affinity chromatography and DEAE anion exchange chromatography. The purified product has a purity of 95% with a yield of 47.3 mg/L of culture. The specific activity of the fusion protein reaches to 2.0 × 107 IU/mg as determined in the CEF/VSV titration system. After excision of the Trx tag by enterokinase, the remaining solo protein was confirmed as rChIFN-α protein by SDS-PAGE, N-terminal sequencing and mass spectrometry. The effects of this Trx-rChIFN-α fusion protein against H9N2 influenza virus infection were also evaluated in ovo. The results showed that the Trx-rChIFN-α protein could significantly reduce the hemagglutination titer of H9N2 virus, and the H9N2 viruses HA gene copy numbers. These findings will enable us to produce large amount and bio-active rChIFN-α protein for future applications.

Analysis of the key networks, metabolic pathways, and regulation substances of hypoxia based on the omics and zebrafish model / 中国药理学与毒理学杂志

OBJECTIVE Hypoxia is associated with many complicated pathophysiological and biochemical processes that integrated and regulated via the key gene, protein and endogenous metabolite levels. Up to date, the exact molecular mechanism of hypoxia still remains unclear. In this work, we further explore the molecular mechanism of hypoxia and adaption to attenuate the damage in zebrafish model that have potential to resist hypoxic environment. METHODS The hypoxic zebrafish model was established in different concentration of oxygen with 3%,5%,10%,21% in water. The brain tissue was separated and the RNA-seq was used to identify the differentially expressed genes. The related endogenous metabolites profiles were obtained by LC-HDMS, and the multivariate statistics was applied to discover the important metabolites candidates in hypoxic zebrafish. The candidates were searched in HMDB, KEGG and Lipid Maps databases. RESULTS The zebrafish hypoxic model was successfully constructed via the different concentration of oxygen, temperature and hypoxic time. The activities of the related hypoxic metabolic enzymes and factors including HIF-1a, actate dehydrogenase (LDH) and citrate synthase (CS) were evaluated. Significant differences (P<0.05 and fold change >2) in the expression of 422 genes were observed between the normal and 3% hypoxic model. Among them, 201 genes increased depended on the lower concentration of oxygen. 53 metabolites were identified that had significant difference between the hypoxia and control groups (P<0.05, fold change>1.5 and VIP>1.5). The ten key metabolites were increased gradually while six compounds were decreased. The endogenous hypoxic metabolites of phenylalanine, D-glucosamine-6P and several important lipids with the relevant hub genes had similar change in hypoxic model. In addition, the metabolic pathways of phenylalanine, glutamine and glycolipid were influenced in both the levels of genes and metabolites. CONCLUSION The up- regulation of phenylalanine, D- glucosamine- 6P and lipid may have further understanding of protective effect in hypoxia. Our data provided an insight to further reveal the hypoxia and adaptation mechanism.

[The application of chemical imaging to detection and enhancement of latent fingerprints].

Chemical imaging (CI) integrates conventional imaging and spectroscopy to attain both spectral and spatial components and structural information from an object simultaneously. Vibrational spectroscopic methods, such as infrared and Raman spectroscopy, combined with imaging are particularly useful. In recent years, CI has found important application in the field of forensic science due to its advantage of highly sensitive, rapid, non-destructive features and it can provide qualitative and quantitative information about specimen at one time. There are many methods for detection and enhancement of latent fingerprints. CI is an emerging platform technology with great potential to visualize latent fingerprints on many objects without any pre-treatment. CI can enhance the quality of the fingerprints developed by conventional methods, then form larger contrast with the background. With the advancement of instruments, the application of CI in the field of fingerprint detection will be more widely used. This paper provides an overview of the principal and classification of CI instrumentation, and reviews the application of CI to detection and enhancement of latent fingerprints. Finally, the direction of CI technology development is viewed.