•Luteolin and chloroquine bind to the main protease of SARS-CoV-2•The binding sites of luteolin are highly consistent with the main protease inhibitors•Luteolin can be used as a potent compound ...against SARS-CoV-2•Binding of luteolin is conducive to the study of antiviral mechanism of traditional Chinese medicine
In the current spread of novel coronavirus (SARS-CoV-2), antiviral drug discovery is of great importance. AutoDock Vina was used to screen potential drugs by molecular docking with the structural protein and non-structural protein sites of new coronavirus. Ribavirin, a common antiviral drug, remdesivir, chloroquine and luteolin were studied. Honeysuckle is generally believed to have antiviral effects in traditional Chinese medicine. In this study, luteolin (the main flavonoid in honeysuckle) was found to bind with a high affinity to the same sites of the main protease of SARS-CoV-2 as the control molecule. Chloroquine has been proved clinically effective and can bind to the main protease; this may be the antiviral mechanism of this drug. The study was restricted to molecular docking without validation by molecular dynamics simulations. Interactions with the main protease may play a key role in fighting against viruses. Luteolin is a potential antiviral molecule worthy of attention.
Trichoderma harzianum strain SQR-T037 is a biocontrol agent that has been shown to enhance the uptake of nutrients (macro- and microelements) by plants in fields. The objective of this study was to ...investigate the contribution of SQR-T037 to P and microelement (Fe, Mn, Cu and Zn) nutrition in tomato plants grown in soil and in hydroponic conditions. Inoculation with SQR-T037 significantly improved the biomass and nutrient uptake of tomato seedlings grown in a nutrient-limiting soil. So we investigated the capability of SQR-T037 to solubilise sparingly soluble minerals in vitro via four known mechanisms: acidification by organic acids, chelation by siderophores, redox by ferric reductase and hydrolysis by phytase. SQR-T037 was able to solubilise phytate, Fe2O3, CuO, and metallic Zn but not Ca3(PO4)2 or MnO2. Organic acids, including lactic acid, citric acid, tartaric acid and succinic acid, were detected by HPLC and LC/MS in two Trichoderma cultures. Additionally, we inoculated tomato seedlings with SQR-T037 using a hydroponic system with specific nutrient deficiencies (i.e., nutrient solutions deficient in P, Fe, Cu or Zn and supplemented with their corresponding solid minerals) to better study the effects of Trichoderma inoculation on plant growth and nutrition. Inoculated seedlings grown in Cu-deficient hydroponic conditions exhibited increases in dry plant biomass (92%) and Cu uptake (42%) relative to control plants. However, we did not observe a significant effect on seedling biomass in plants grown in the Fe- and Zn-deficient hydroponic conditions; by contrast, the biomass decreased by 82% in the P-deficient hydroponic condition. Thus, we demonstrated that Trichoderma SQR-T037 competed for P (phytate) and Zn with tomato seedlings by suppressing root development, releasing phytase and/or chelating minerals. The results of this study suggest that the induction of increased or suppressed plant growth occurs through the direct effect of T. harzianum on root development, in combination with indirect mechanisms, such as mineral solubilisation (including solubilisation via acidification, redox, chelation and hydrolysis).
There has been suggestive evidence of intermediate-mass black holes (IMBHs; 103−5 M ) existing in some globular clusters (GCs) and dwarf galaxies, but IMBHs as a population remain elusive. As a ...main-sequence star passes too close by an IMBH it might be tidally captured and disrupted. We study the long-term accretion and observational consequence of such tidal disruption events. The disruption radius is hundreds to thousands of the BH's Schwarzschild radius, so the circularization of the falling-back debris stream is very inefficient due to weak general relativity effects. Due to this and a high mass fallback rate, the bound debris initially goes through a ∼10 yr long super-Eddington accretion phase. The photospheric emission of the outflow ejected during this phase dominates the observable radiation and peaks in the UV/optical bands with a luminosity of . After the accretion rate drops below the Eddington rate, the bolometric luminosity follows the conventional t−5/3 power-law decay, and X-rays from the inner accretion disk start to be seen. Modeling the newly reported IMBH tidal disruption event candidate 3XMM J2150-0551, we find a general consistency between the data and predictions. The search for these luminous, long-term events in GCs and nearby dwarf galaxies could unveil the IMBH population.
Abstract
During the inspiralling of a white dwarf (WD) into an intermediate-mass black hole (∼10
2−5
M
⊙
), both gravitational waves (GWs) and electromagnetic (EM) radiation are emitted. Once the ...eccentric orbit’s pericenter radius approaches the tidal radius, the WD would be tidally stripped upon each pericenter passage. The accretion of this stripped mass would produce EM radiation. It is suspected that the recently discovered new types of transients, namely the quasiperiodic eruptions and the fast ultraluminous x-ray bursts, might originate from such systems. Modeling these flares requires a prediction of the amount of stripped mass from the WD and the details of the mass supply to the accretion disk. We run hydrodynamical simulations to study the orbital parameter dependence of the stripped mass. We find that our results match the analytical estimate that the stripped mass is proportional to
z
5/2
, where
z
is the excess depth by which the WD overfills its instantaneous Roche lobe at the pericenter. The corresponding fallback rate of the stripped mass is calculated, which may be useful in interpreting the individual flaring light curve in candidate EM sources. We further calculate the long-term mass-loss evolution of a WD during its inspiral and the detectability of the GW and EM signals. The EM signal from the mass-loss stage can be easily detected: the limiting distance is ∼320(
M
h
/10
4
M
⊙
) Mpc for the Einstein Probe. The GW signal, for space-borne detectors such as Laser Interferometer Space Antenna or TianQin, can be detected only within the Local Supercluster (∼33 Mpc).
Pharmacological interactions are useful for understanding ligand binding mechanisms of a therapeutic target. These interactions are often inferred from a set of active compounds that were acquired ...experimentally. Moreover, most docking programs loosely coupled the stages (binding-site and ligand preparations, virtual screening, and post-screening analysis) of structure-based virtual screening (VS). An integrated VS environment, which provides the friendly interface to seamlessly combine these VS stages and to identify the pharmacological interactions directly from screening compounds, is valuable for drug discovery.
We developed an easy-to-use graphic environment, iGEMDOCK, integrating VS stages (from preparations to post-screening analysis). For post-screening analysis, iGEMDOCK provides biological insights by deriving the pharmacological interactions from screening compounds without relying on the experimental data of active compounds. The pharmacological interactions represent conserved interacting residues, which often form binding pockets with specific physico-chemical properties, to play the essential functions of a target protein. Our experimental results show that the pharmacological interactions derived by iGEMDOCK are often hot spots involving in the biological functions. In addition, iGEMDOCK provides the visualizations of the protein-compound interaction profiles and the hierarchical clustering dendrogram of the compounds for post-screening analysis.
We have developed iGEMDOCK to facilitate steps from preparations of target proteins and ligand libraries toward post-screening analysis. iGEMDOCK is especially useful for post-screening analysis and inferring pharmacological interactions from screening compounds. We believe that iGEMDOCK is useful for understanding the ligand binding mechanisms and discovering lead compounds. iGEMDOCK is available at http://gemdock.life.nctu.edu.tw/dock/igemdock.php.
Abstract
Short-duration gamma-ray bursts (sGRBs) are commonly attributed to the mergers of double neutron stars (NSs) or the mergers of a neutron star with a black hole (BH). While the former ...scenario was confirmed by the event GW170817, the latter remains elusive. Here, we consider the latter scenario in which an NS is tidally disrupted by a fast-spinning low-mass BH and the accretion onto the BH launches a relativistic jet and hence produces an sGRB. The merging binary’s orbit is likely misaligned with the BH’s spin. Hence, the Lense–Thirring precession around the BH may cause a hyperaccreting thick disk to precess in a solid-body manner. We propose that a jet, initially aligned with the BH spin, is deflected and collimated by the wind from the disk, therefore being forced to precess along with the disk. This would result in a quasiperiodic oscillation or modulation in the gamma-ray light curve of the sGRB, with a quasi-period of ∼0.01–0.1 s. The appearance of the modulation may be delayed respective to the triggering of the light curve. This feature, unique to the BH–NS merger, may have already revealed itself in a few observed sGRBs (such as GRB 130310A), and it carries the spin–orbit orientation information of the merging system. Identification of this feature would be a new approach to reveal spin–orbit misaligned merging BH–NS systems, which are likely missed by the current gravitational-wave searching strategy that is principally targeting aligned systems.
Two X-ray sources were recently discovered by Irwin et al. that are compact companions to elliptical galaxies showing ultraluminous flares with fast rise (∼minute) and decay (∼hour), and with a peak ...luminosity ∼1040-41 erg s−1. Together with two other sources found earlier, they constitute a new type of fast transients that cannot be attributed to neutron stars, but might be due to intermediate-mass black holes (IMBHs; ). The flaring behavior is recurrent for at least two sources. If the flare represents a short period of accretion onto an IMBH during the periastron passage of a donor star on an eccentric (i.e., repeating) or parabolic (non-repeating) orbit, we argue that the flare's rise time corresponds to the duration during which the donor's tidally stripped mass joins a residual disk at the pericenter. This duration is in turn equal to three other timescales: the duration of stripping, the sound crossing time of the donor, and the circular orbit time at the pericenter radius. Only a white dwarf (WD) can have a sound crossing time as short as one minute. Therefore, the donor must be a WD and it was stripped of ∼10−10 M upon each passage at several to tens of Schwarzschild radii from the IMBH. The flux decay corresponds to the viscous drainage of the supplied mass toward the hole. Aided by long-term X-ray monitoring, this type of fast transient would be an ideal target for next-generation gravitational wave detectors.
SARS-CoV-2 variants of concern (VOC) B.1.1.7 (alpha) and B.1.351 (beta) show increased transmissibility and enhanced antibody neutralization resistance. Here we demonstrate in K18-hACE2 transgenic ...mice that B.1.1.7 and B.1.351 are 100-fold more lethal than the original SARS-CoV-2 bearing 614D. B.1.1.7 and B.1.351 cause more severe organ lesions in K18-hACE2 mice than early SARS-CoV-2 strains bearing 614D or 614G, with B.1.1.7 and B.1.351 infection resulting in distinct tissue-specific cytokine signatures, significant D-dimer depositions in vital organs and less pulmonary hypoxia signaling before death. However, K18-hACE2 mice with prior infection of early SARS-CoV-2 strains or intramuscular immunization of viral spike or receptor binding domain are resistant to the lethal reinfection of B.1.1.7 or B.1.351, despite having reduced neutralization titers against these VOC than early strains. Our results thus distinguish pathogenic patterns in K18-hACE2 mice caused by B.1.1.7 and B.1.351 infection from those induced by early SARS-CoV-2 strains, and help inform potential medical interventions for combating COVID-19.
Coastal saline soil is an important reserve land resource that has high potential for agricultural utilization. The present study adopted a high-throughput absolute quantification 16S rRNA sequencing ...method to investigate the effect of four different fertilization regimes (namely 100% of bio-organic fertilizer, 70% of bio-organic fertilizer +30% of chemical fertilizer, 30% of bio-organic fertilizer +70% of chemical fertilizer, and 100% of chemical fertilizer) on bacterial community assembly in a tomato cultivated saline soil. The results from the field experiment showed that a combination of 70% bio-organic fertilizer plus 30% of chemical fertilizer was the optimal dose to develop tomato cultivation (for improving yield and fruit quality) in this coastal tidal zone. The pot experiment gave the similar results on tomato growth and indicated the application of 70% bio-organic fertilizer plus 30% of chemical fertilizer as the best treatment to active the soil microbiome. The input of nutrients by fertilizers increased the total abundance of bacteria (to >3 fold compared to the initial soil) and simultaneously led to a significant loss of bacterial diversity in soil. The predominant phyla including Proteobacteria, Bacteroidetes and Firmicutes were the main contributors in the microbiome shift especially shown by their remarkable enrichment in the soil that treated by 70% of bio-organic fertilizer and those by the 100% chemical fertilizer. The RDA and Pearson correlation analyses indicated that the soil nutrient availability, especially available P and K, and soil salinity were the key environmental factors that shaped the bacterial community in this ecosystem, though the organic matter content and soil pH also played important roles in microbiome assembly.
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•Bacterial absolute abundance in saline soil increases >3 folds in all four fertilization regimes.•Bacterial diversity in saline soil decreases significantly in all fertilizer-applied samples.•Soil salinity and nutrient availability (P and K) play key roles in shaping bacterial community.•70% bio-organic fertilizer plus 30% of chemical fertilizer is the optimal dose for tomato growth.•Absolute 16S-seq allows more precise investigation on microbial dynamics across multi samples.
Abstract ASASSN-14ko was identified as an abnormal periodic nuclear transient with a potential decreasing period. Its outbursts in the optical and UV bands have displayed a consistent and smooth ...“fast rise and slow decay” pattern since its discovery, which has recently experienced an unexpected alteration in the last two epochs, as revealed by our proposed high-cadence Swift observations. The new light curve profiles show a bump during the rising stages and a rebrightening during the declining stages, making them much broader and symmetrical than the previous ones. In the last two epochs, there is no significant difference in the X-ray spectral slope compared to the previous one, and its overall luminosity is lower than those of the previous epochs. The energy released in the early bump and rebrightening phases (∼10 50 erg) could be due to collision of the stripped stream from partial tidal disruption events with an expanded accretion disk. We also discussed other potential explanations, such as disk instability and star–disk collisions. Further high-cadence multiwavelength observations of subsequent cycles are encouraged to comprehend the unique periodic source with its new intriguing features.
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