Regulation of HIV-1 Gag-Pol Expression by Shiftless, an Inhibitor of Programmed -1 Ribosomal Frameshifting.

Programmed -1 ribosomal frameshifting (-1PRF) is a widely used translation recoding mechanism. HIV-1 expresses Gag-Pol protein from the Gag-coding mRNA through -1PRF, and the ratio of Gag to Gag-Pol is strictly maintained for efficient viral replication. Here, we report that the interferon-stimulated gene product C19orf66 (herein named Shiftless) is a host factor that inhibits the -1PRF of HIV-1. Shiftless (SFL) also inhibited the -1PRF of a variety of mRNAs from both viruses and cellular genes. SFL interacted with the -1PRF signal of target mRNA and translating ribosomes and caused premature translation termination at the frameshifting site. Downregulation of translation release factor eRF3 or eRF1 reduced SFL-mediated premature translation termination. We propose that SFL binding to target mRNA and the translating ribosome interferes with the frameshifting process. These findings identify SFL as a broad-spectrum inhibitor of -1PRF and help to further elucidate the mechanisms of -1PRF.

Identification of SARS-CoV-2 inhibitors using lung and colonic organoids.

There is an urgent need to create novel models using human disease-relevant cells to study severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) biology and to facilitate drug screening. Here, as SARS-CoV-2 primarily infects the respiratory tract, we developed a lung organoid model using human pluripotent stem cells (hPSC-LOs). The hPSC-LOs (particularly alveolar type-II-like cells) are permissive to SARS-CoV-2 infection, and showed robust induction of chemokines following SARS-CoV-2 infection, similar to what is seen in patients with COVID-19. Nearly 25% of these patients also have gastrointestinal manifestations, which are associated with worse COVID-19 outcomes1. We therefore also generated complementary hPSC-derived colonic organoids (hPSC-COs) to explore the response of colonic cells to SARS-CoV-2 infection. We found that multiple colonic cell types, especially enterocytes, express ACE2 and are permissive to SARS-CoV-2 infection. Using hPSC-LOs, we performed a high-throughput screen of drugs approved by the FDA (US Food and Drug Administration) and identified entry inhibitors of SARS-CoV-2, including imatinib, mycophenolic acid and quinacrine dihydrochloride. Treatment at physiologically relevant levels of these drugs significantly inhibited SARS-CoV-2 infection of both hPSC-LOs and hPSC-COs. Together, these data demonstrate that hPSC-LOs and hPSC-COs infected by SARS-CoV-2 can serve as disease models to study SARS-CoV-2 infection and provide a valuable resource for drug screening to identify candidate COVID-19 therapeutics.

Human organoid models to study SARS-CoV-2 infection.

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the deadliest pandemics in history. SARS-CoV-2 not only infects the respiratory tract, but also causes damage to many organs. Organoids, which can self-renew and recapitulate the various physiology of different organs, serve as powerful platforms to model COVID-19. In this Perspective, we overview the current effort to apply both human pluripotent stem cell-derived organoids and adult organoids to study SARS-CoV-2 tropism, host response and immune cell-mediated host damage, and perform drug discovery and vaccine development. We summarize the technologies used in organoid-based COVID-19 research, discuss the remaining challenges and provide future perspectives in the application of organoid models to study SARS-CoV-2 and future emerging viruses.

A novel antimicrobial peptide S24 combats serious wound infections caused by Pseudomonas aeruginosa and Acinetobacter baumannii.

OBJECTIVES: Pseudomonas aeruginosa and Acinetobacter baumannii are ranked as top-priority organisms by WHO. Antimicrobial peptides (AMPs) are promising antimicrobial agents that are highly effective against serious bacterial infections. METHODS: In our previous study, a series of α-helical AMPs were screened using a novel multiple-descriptor strategy. The current research suggested that S24 exhibited strong antimicrobial activity against major pathogenic bacteria, and displayed minimal haemolysis, good serum stability and maintained salt resistance. RESULTS: We found that S24 exerted an antimicrobial effect by destroying outer membrane permeability and producing a strong binding effect on bacterial genomic DNA that inhibits genomic DNA migration. Furthermore, S24 exerted a strong ability to promote healing in wound infected by P. aeruginosa, A. baumannii and mixed strains in a mouse model. CONCLUSIONS: Overall, S24 showed good stability under physiological conditions and excellent antimicrobial activity, suggesting it may be a potential candidate for the development of serious bacterial infection treatment.

Glycosyltransferase Slr1064 regulates carbon metabolism by modulating the levels of UDP-GlcNAc in Synechocystis sp. PCC 6803.

Glycosyltransferases (GTs) are enzymes that transfer sugars to various targets. They play important roles in diverse biological processes, including photosynthesis, cell motility, exopolysaccharide biosynthesis, and lipid metabolism; however, their involvement in regulating carbon metabolism in Synechocystis sp. PCC 6803 has not been reported. We identified a novel GT protein, Slr1064, involved in carbon metabolism. The effect of slr1064 deletion on the growth of Synechocystis cells and functional mechanisms of Slr1064 on carbon metabolism were thoroughly investigated through physiological, biochemistry, proteomic, and metabolic analyses. We found that this GT, which is mainly distributed in the membrane compartment, is essential for the growth of Synechocystis under heterotrophic and mixotrophic conditions, but not under autotrophic conditions. The deletion of slr1064 hampers the turnover rate of Gap2 under mixotrophic conditions and disrupts the assembly of the PRK/GAPDH/CP12 complex under dark culture conditions. Additionally, UDP-GlcNAc, the pivotal metabolite responsible for the O-GlcNAc modification of GAPDH, is downregulated in the Δslr1064. Our work provides new insights into the role of GTs in carbon metabolism in Synechocystis and elucidate the mechanism by which carbon metabolism is regulated in this important model organism.

SARS-CoV-2 Infection Induces Ferroptosis of Sinoatrial Node Pacemaker Cells.

BACKGROUND: Increasing evidence suggests that cardiac arrhythmias are frequent clinical features of coronavirus disease 2019 (COVID-19). Sinus node damage may lead to bradycardia. However, it is challenging to explore human sinoatrial node (SAN) pathophysiology due to difficulty in isolating and culturing human SAN cells. Embryonic stem cells (ESCs) can be a source to derive human SAN-like pacemaker cells for disease modeling. METHODS: We used both a hamster model and human ESC (hESC)-derived SAN-like pacemaker cells to explore the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on the pacemaker cells of the heart. In the hamster model, quantitative real-time polymerase chain reaction and immunostaining were used to detect viral RNA and protein, respectively. We then created a dual knock-in SHOX2:GFP;MYH6:mCherry hESC reporter line to establish a highly efficient strategy to derive functional human SAN-like pacemaker cells, which was further characterized by single-cell RNA sequencing. Following exposure to SARS-CoV-2, quantitative real-time polymerase chain reaction, immunostaining, and RNA sequencing were used to confirm infection and determine the host response of hESC-SAN-like pacemaker cells. Finally, a high content chemical screen was performed to identify drugs that can inhibit SARS-CoV-2 infection, and block SARS-CoV-2-induced ferroptosis. RESULTS: Viral RNA and spike protein were detected in SAN cells in the hearts of infected hamsters. We established an efficient strategy to derive from hESCs functional human SAN-like pacemaker cells, which express pacemaker markers and display SAN-like action potentials. Furthermore, SARS-CoV-2 infection causes dysfunction of human SAN-like pacemaker cells and induces ferroptosis. Two drug candidates, deferoxamine and imatinib, were identified from the high content screen, able to block SARS-CoV-2 infection and infection-associated ferroptosis. CONCLUSIONS: Using a hamster model, we showed that primary pacemaker cells in the heart can be infected by SARS-CoV-2. Infection of hESC-derived functional SAN-like pacemaker cells demonstrates ferroptosis as a potential mechanism for causing cardiac arrhythmias in patients with COVID-19. Finally, we identified candidate drugs that can protect the SAN cells from SARS-CoV-2 infection.

An Immuno-Cardiac Model for Macrophage-Mediated Inflammation in COVID-19 Hearts.

[Figure: see text].

Reference values of impulse oscillometry (IOS) for healthy Chinese children aged 4-17 years.

OBJECTIVE: To establish the predicted value of pulmonary function determined by impulse oscillometry (IOS) in children (4-17 years old) in China. METHODS: A total of 6270 healthy children aged 4-17 years in China were included. The Master Screen IOS pulmonary function device (Jaeger Co, Germany) was used to detect the respiratory impedance (Zrs), resonant frequency (Fres), respiratory system resistance (Rrs) and respiratory system reactance (Xrs) at various oscillation frequencies, and the indices above were analysed. Stepwise multivariate regression was used to establish the regression equation of related parameters of IOS in different sexes, ages, height, and weight. RESULTS: The differences in the main IOS parameters between different age stages were statistically significant regardless of sex (P < 0.05). The stepwise multivariate regression analysis showed that IOS parameters were related to height, age, and weight, and most IOS parameters were most closely related to height (the absolute value of the regression coefficient was the largest). With increasing age and height, the values of Z5, R5, R20, R5-R20, and Fres decreased, while the value of X5 increased. Through height, age, and weight, we obtained the normal predicted values equation of children's IOS parameters. Compared with the other reference equations, our reference equation is more suitable for Chinese children. CONCLUSIONS: The study revealed the reference values of IOS parameters in healthy Chinese children. In the evaluation of results for lung function measurements, this predicted value equation is more consistent with the characteristics of Chinese children than other reference equations. CLINICAL TRIAL: ChiCTR: 1800019029.

Characterization of Per- and Polyfluorinated Alkyl Substances Present in Commercial Anti-fog Products and Their In Vitro Adipogenic Activity.

Anti-fog sprays and solutions are used on eyeglasses to minimize the condensation of water vapor, particularly while wearing a mask. Given their water-repellent properties, we sought to characterize per- and polyfluorinated alkyl substance (PFAS) compounds in four anti-fog spray products, five anti-fog cloth products, and two commercial fluorosurfactant formulations suspected to be used in preparing anti-fog products. Fluorotelomer alcohols (FTOHs) and fluorotelomer ethoxylates (FTEOs) were detected in all products and formulations. While 6:2 FTOH and the 6:2 FTEO polymeric series were predominant, one anti-fog cloth and one formulation contained 8:2, 10:2, 12:2, 14:2, and 16:2 FTOH and FTEO polymeric series. PFAS concentrations varied in samples and were detected at levels up to 25,000 µg/mL in anti-fog sprays and 185,000 µg (g cloth)-1 in anti-fog cloth products. The total organic fluorine (TOF) measurements of anti-fog products ranged from 190 to 20,700 µg/mL in sprays and 44,200 to 131,500 µg (g cloth)-1 in cloths. Quantified FTOHs and FTEOs accounted for 1-99% of TOF mass. In addition, all four anti-fog sprays and both commercial formulations exhibited significant cytotoxicity and adipogenic activity (either triglyceride accumulation and/or pre-adipocyte proliferation) in murine 3T3-L1 cells. Results suggest that FTEOs are a significant contributor to the adipogenic activity exhibited by the anti-fog sprays. Altogether, these results suggest that FTEOs are present in commercial products at toxicologically relevant levels, and more research is needed to fully understand the health risks from using these PFAS-containing products.

Diagnostic utility of pleural cell-free nucleic acids in undiagnosed pleural effusions.

Pleural effusion (PE) is a common sign caused by various disorders. Microbiology, histology and cytology are reference standards for these disorders. However, these diagnostic tools have limitations, including invasiveness, high cost, long turnaround time, and observer-dependent. Soluble biomarkers in pleural fluid (PF) are promising diagnostic tools because they are mininvasive, economical, and objective. Recent studies have revealed that some cell-free nucleic acids (e.g., DNA, mRNA, microRNA, and lncRNA) in PF are potential diagnostic markers for many disorders. Here, we review the performance of PF cell-free nucleic acids for differentiating and stratification of PE.

Identifying FDA-approved drugs with multimodal properties against COVID-19 using a data-driven approach and a lung organoid model of SARS-CoV-2 entry.

BACKGROUND: Vaccination programs have been launched worldwide to halt the spread of COVID-19. However, the identification of existing, safe compounds with combined treatment and prophylactic properties would be beneficial to individuals who are waiting to be vaccinated, particularly in less economically developed countries, where vaccine availability may be initially limited. METHODS: We used a data-driven approach, combining results from the screening of a large transcriptomic database (L1000) and molecular docking analyses, with in vitro tests using a lung organoid model of SARS-CoV-2 entry, to identify drugs with putative multimodal properties against COVID-19. RESULTS: Out of thousands of FDA-approved drugs considered, we observed that atorvastatin was the most promising candidate, as its effects negatively correlated with the transcriptional changes associated with infection. Atorvastatin was further predicted to bind to SARS-CoV-2's main protease and RNA-dependent RNA polymerase, and was shown to inhibit viral entry in our lung organoid model. CONCLUSIONS: Small clinical studies reported that general statin use, and specifically, atorvastatin use, are associated with protective effects against COVID-19. Our study corroborrates these findings and supports the investigation of atorvastatin in larger clinical studies. Ultimately, our framework demonstrates one promising way to fast-track the identification of compounds for COVID-19, which could similarly be applied when tackling future pandemics.

Understanding the relative performance of SCAN, SIM, PMRM and MRM methods for quantifying polycyclic aromatic hydrocarbons in crude oil samples.

RATIONALE: Polycyclic aromatic hydrocarbons (PAHs) present in oil spill samples are analyzed by gas chromatography/mass spectrometry (GC/MS) and gas chromatography/tandem mass spectrometry (GC/MS/MS) using four different methods: (1) full scan (SCAN), (2) selected ion monitoring (SIM), (3) multiple reaction monitoring (MRM), and (4) pseudo multiple reaction monitoring (PMRM). This study quantifies the relative performance of these methods. METHODS: Novel experiments were designed to measure the signal-to-noise (S/N) ratios of all four methods. This was accomplished by spiking the crude oil with five deuterated PAHs (dPAHs) in two distinct ways: (1) varying the background noise by changing crude oil concentrations before spiking the samples with 1 ng/mL of dPAHs, and (2) varying the signal by spiking dPAHs concentrations of 0.5 and 5 ng/mL into a crude oil sample. RESULTS: The MRM method is the most selective and sensitive of the four methods. It also provides the lowest limit of detection (LOD) and limit of quantitation (LOQ). MRM is the optimal approach for quantifying PAHs in complex petroleum samples containing high levels of background noise. Also, our data show that the PAHs in complex oil spill samples can be quantified by MRM without using any complicated sample preparation steps. CONCLUSIONS: Based on our experimental data, the relative performance of the four methods used for quantifying PAHs in crude oil samples can be ranked as MRM > PMRM > SIM > SCAN.

Fabrication and characterization of SiC/Ge/graphene heterojunction with Ge micro-nano structures.

To widen the detection wavelength range and improve the detection sensitivity of SiC-based optoelectronic devices, the SiC/Ge/graphene heterojunction was fabricated by using wet transfer of the graphene following chemical vapor deposition. The Ge films on 4H-SiC(0001) have polycrystalline structure with nano-wire (NWs) and submicron spherical island (SIs) features. Due to the distinct light trapping effect of the Ge NWs, the SiC/GeNWs/graphene heterojunction has an absorbance of more than 90% in the 500-1600 nm range, which is higher than the SiC/GeSIs/graphene heterojunction. And the SiC/GeNWs/graphene heterojunction photodetector exhibits rectification ratio up to 25 at ±2 V and stable photoresponse to the NIR light at zero voltage bias.

[Features of lung dysfunction in children with Mycoplasma pneumoniae pneumonia with different chest imaging findings].

OBJECTIVE: To explore the features of pulmonary dysfunction in children with Mycoplasma pneumoniae pneumonia (MPP) with different chest imaging findings. METHODS: The clinical data from 215 children with MPP were reviewed. These patients were grouped based on chest image findings (bronchopneumonia, n=125; lobar pneumonia, n=69; interstitial pneumonia, n=21). Lung function parameters including forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC), peak expiratory flow (PEF), and the maximum mid-expiratory flow rate (MMEF 25%-75%) were compared between the groups. RESULTS: In the acute stage, patients with bronchopneumonia had significantly lower PEF values (measured value and measured value/predicted value) than the other two groups of patients, children with lobar pneumonia had a significant lower MMEF 25%-75% than other patients, and children with interstitial pneumonia had a significantly lower FVC. All patients experienced an improvement in lung function parameters except FEV1 of the lobar pneumonia group in the recovery stage. CONCLUSIONS: Various features of pulmonary dysfunction can be observed among children with MPP with different chest imaging findings. Patients with bronchopneumonia mainly exhibit large airway dysfunction. The ones with lobar pneumonia mainly suffer small airway dysfunction, and those with interstitial pneumonia demonstrate both airway obstruction and restrictive ventilatory dysfunction.

Effects of low-molecular-weight organic acids on the transformation and phosphate retention of iron (hydr)oxides.

The retention and mobilization of phosphate in soils are closely associated with the adsorption of iron (hydr)oxides and root exudation of low-molecular-weight organic acids (LMWOAs). This study investigated the role of LMWOAs in phosphate mobilization under incubation and field conditions. LMWOAs-mediated iron (hydr)oxide transformation and phosphate adsorption experiments revealed that the presence of LMWOAs decreased the phosphate adsorption capacity of iron (hydr)oxides by up to ~74 % due to the competition effect, while LMWOAs-induced iron mineral transformation resulted in an approximately six-fold increase in phosphate retention by decreasing the crystallinity and increasing the surface reactivity. Root simulation in rhizobox experiments demonstrated that LMWOAs can alter the contents of different extractable phosphate species and iron components, leading to 10 % ~ 30 % decreases in available phosphate in the near root region of two tested soils. Field experiments showed that crop covering between mango tree rows promoted the exudation of LMWOAs from mango roots. In addition, crop covering increased the contents of total phosphate and available phosphate by 9.08 % ~ 61.20 % and 34.33 % ~ 147.33 % in the rhizosphere soils of mango trees, respectively. These findings bridge the microscale and field scale to understand the delicate LMWOAs-mediated balance between the retention and mobilization of phosphate on iron (hydr)oxide surface, thereby providing important implications for mitigating the low utilization efficiency of phosphate in iron-rich soils.

MODMS: a multi-omics database for facilitating biological studies on alfalfa (Medicago sativa L.).

Alfalfa (Medicago sativa L.) is a globally important forage crop. It also serves as a vegetable and medicinal herb because of its excellent nutritional quality and significant economic value. Multi-omics data on alfalfa continue to accumulate owing to recent advances in high-throughput techniques, and integrating this information holds great potential for expediting genetic research and facilitating advances in alfalfa agronomic traits. Therefore, we developed a comprehensive database named MODMS (multi-omics database of M. sativa) that incorporates multiple reference genomes, annotations, comparative genomics, transcriptomes, high-quality genomic variants, proteomics, and metabolomics. This report describes our continuously evolving database, which provides researchers with several convenient tools and extensive omics data resources, facilitating the expansion of alfalfa research. Further details regarding the MODMS database are available at https://modms.lzu.edu.cn/.

Chromosome-level genome assembly of Pedicularis kansuensis illuminates genome evolution of facultative parasitic plant.

Parasitic plants have a heterotrophic lifestyle, in which they withdraw all or part of their nutrients from their host through the haustorium. Despite the release of many draft genomes of parasitic plants, the genome evolution related to the parasitism feature of facultative parasites remains largely unknown. In this study, we present a high-quality chromosomal-level genome assembly for the facultative parasite Pedicularis kansuensis (Orobanchaceae), which invades both legume and grass host species in degraded grasslands on the Qinghai-Tibet Plateau. This species has the largest genome size compared with other parasitic species, and expansions of long terminal repeat retrotransposons accounting for 62.37% of the assembly greatly contributed to the genome size expansion of this species. A total of 42,782 genes were annotated, and the patterns of gene loss in P. kansuensis differed from other parasitic species. We also found many mobile mRNAs between P. kansuensis and one of its host species, but these mobile mRNAs could not compensate for the functional losses of missing genes in P. kansuensis. In addition, we identified nine horizontal gene transfer (HGT) events from rosids and monocots, as well as one single-gene duplication events from HGT genes, which differ distinctly from that of other parasitic species. Furthermore, we found evidence for HGT through transferring genomic fragments from phylogenetically remote host species. Taken together, these findings provide genomic insights into the evolution of facultative parasites and broaden our understanding of the diversified genome evolution in parasitic plants and the molecular mechanisms of plant parasitism.

SARS-CoV-2 infection causes dopaminergic neuron senescence.

COVID-19 patients commonly present with signs of central nervous system and/or peripheral nervous system dysfunction. Here, we show that midbrain dopamine (DA) neurons derived from human pluripotent stem cells (hPSCs) are selectively susceptible and permissive to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. SARS-CoV-2 infection of DA neurons triggers an inflammatory and cellular senescence response. High-throughput screening in hPSC-derived DA neurons identified several FDA-approved drugs that can rescue the cellular senescence phenotype by preventing SARS-CoV-2 infection. We also identified the inflammatory and cellular senescence signature and low levels of SARS-CoV-2 transcripts in human substantia nigra tissue of COVID-19 patients. Furthermore, we observed reduced numbers of neuromelanin+ and tyrosine-hydroxylase (TH)+ DA neurons and fibers in a cohort of severe COVID-19 patients. Our findings demonstrate that hPSC-derived DA neurons are susceptible to SARS-CoV-2, identify candidate neuroprotective drugs for COVID-19 patients, and suggest the need for careful, long-term monitoring of neurological problems in COVID-19 patients.