Ligand recognition and G-protein coupling of trace amine receptor TAAR1.

Trace-amine-associated receptors (TAARs), a group of biogenic amine receptors, have essential roles in neurological and metabolic homeostasis1. They recognize diverse endogenous trace amines and subsequently activate a range of G-protein-subtype signalling pathways2,3. Notably, TAAR1 has emerged as a promising therapeutic target for treating psychiatric disorders4,5. However, the molecular mechanisms underlying its ability to recognize different ligands remain largely unclear. Here we present nine cryo-electron microscopy structures, with eight showing human and mouse TAAR1 in a complex with an array of ligands, including the endogenous 3-iodothyronamine, two antipsychotic agents, the psychoactive drug amphetamine and two identified catecholamine agonists, and one showing 5-HT1AR in a complex with an antipsychotic agent. These structures reveal a rigid consensus binding motif in TAAR1 that binds to endogenous trace amine stimuli and two extended binding pockets that accommodate diverse chemotypes. Combined with mutational analysis, functional assays and molecular dynamic simulations, we elucidate the structural basis of drug polypharmacology and identify the species-specific differences between human and mouse TAAR1. Our study provides insights into the mechanism of ligand recognition and G-protein selectivity by TAAR1, which may help in the discovery of ligands or therapeutic strategies for neurological and metabolic disorders.

Soil microbiota associated with immune-mediated disease was influenced by heavy metal stress in roadside soils of Shanghai.

Heavy metals (HMs) and total petroleum hydrocarbons (TPHs) in soils can be detrimental to both soil microorganisms and public health. However, the effects of HMs and TPHs on microbes as well as the consequent microbial-derived health risk remains unclear in soils by local roads where citizens are clearly accessible to traffic-derived pollutants. Herein, we sampled 84 roadside soils throughout Shanghai. We measured the levels of soil edaphic factors, 6 HMs, and alkane TPHs. We further focused on the responses of bacterial and fungal communities assessed via sequencing and network analysis. Results showed that all soil HMs exceeded background levels of Shanghai soil, while the levels of TPHs are comparable to unpolluted sites. Bacterial network nodes and links decreased sharply under HM stress whereas that of fungal networks remained unchanged. The differential pattern was attributed to the asynchronous response of key classes that fungal key classes were more resistant to HMs than bacteria. In addition, 66.8 % of fungal genera associated with immune-mediated disease increased with increased HM stress for its HM tolerance. Together our findings indicate that despite the relatively stable fungal community in response to environmental stresses, the elevation of harmful fungi likely pose threats to health of urban dwellers.

A Pipeline to Investigate the Structures and Signaling Pathways of Sphingosine 1-Phosphate Receptors.

Lysophospholipids (LPLs) are bioactive lipids that include sphingosine 1-phosphate (S1P), lysophosphatidic acid, etc. S1P, a metabolic product of sphingolipids in the cell membrane, is one of the best-characterized LPLs that regulates a variety of cellular physiological responses via signaling pathways mediated by sphingosine 1-phosphate receptors (S1PRs). This implicated that the S1P-S1PRs signaling system is a remarkable potential therapeutic target for disorders, including multiple sclerosis (MS), autoimmune disorders, cancer, inflammation, and even COVID-19. S1PRs, a small subset of the class A G-protein coupled receptor (GPCR) family, are composed of five subtypes: S1PR1, S1PR2, S1PR3, S1PR4, and S1PR5. The lack of detailed structural information, however, impedes the drug discovery targeting S1PRs. Here, we applied the cryo-electron microscopy method to solve the structure of the S1P-S1PRs complex, and elucidated the mechanism of activation, selective drug recognition, and G-protein coupling by using cell-based functional assays. Other lysophospholipid receptors (LPLRs) and GPCRs can also be studied using this strategy.

Karst rocky desertification diverged the soil residing and the active ectomycorrhizal fungal communities thereby fostering distinctive extramatrical mycelia.

Ectomycorrhizal fungi (EMF) are mutualists that play crucial roles in liberation, nutrient acquisition, transfer of growth-limiting resources and provision of water to host plants in terrestrial ecosystems, particularly in stressed prone climates. In this study, a field-based experiment was performed in Yunnan, China to assess the effect of karst rocky desertification (KRD) and natural forests (non-KRD) sites on the richness and composition of EMF communities. Inert sand-filled mesh bags were employed to characterize the active EMF and quantify the production of extramatrical mycelium (EMM). Results indicated that, EMF exhibited a significant differentiation among KRD and non-KRD sites, richness and diversity were higher across KRD areas, whereas the evenness showed the opposite trend. Ascomycota and Zygomycota were greater across KRD sites, however, Basidiomycota showed no difference across both study sites. The relative abundance of Clavaria, Butyriboletus, Odontia, Phyloporus, Helvella, Russula and Tomentella were higher across the KRD sites, whereas, Clavulinopsis, Endogone, Amanita, Inocybe and Clavulina were higher across the non-KRD sites. It's worth noting that, saprophytic (SAP) fungal community was found to be more abundant in the soil than the mesh bags at both sites particularly at KRD sites, which likely provide more free space and less competition for the EMF to thrive well in the mesh bags. In similar pattern, ergosterol concentration in mesh bags was observed relatively higher at KRD sites than the non-KRD sites. The Entoloma, Amanita, and Sebacina were found to be substantially higher in mesh bags than soil across both sites. Delicatula, Helvella and Tomentella on the other hand, showed higher relative abundance in mesh bags than soil over KRD sites, however they did not differ across non-KRD sites. Taken together, the presented results highlight relationship between the EMF community and the complex KRD environment, which is very important for the restoration of disturbed karst landscapes.

Immune-mediated disease associated microbial community responded to PAH stress in phyllosphere of roadside greenspaces in Shanghai.

Microorganisms in urban greenspaces play key roles in ecosystem service provision and potentially influence human health. Increasing evidence suggests that anthropogenic disturbance poses constant stress on urban microbial communities, yet, as previous studies have focused on non-contaminated greenspaces, it has remained largely unknown how microorganisms respond to anthropogenic stress in roadside greenspaces with contamination. Our previous effort determined phyllosphere PAHs of camphor trees in 84 sites of roadside greenspaces along the urban-rural gradient in Shanghai. Here, we further investigated the phyllosphere microbial communities (PMCs) of the same sites across the same urban categories, including urban, suburban, and rural areas using high-throughput DNA sequencing. We aimed to explore how PMCs, especially those associated with immune-mediated diseases (IMDs), were affected by PAHs and the surrounding land-use types. We found that several microorganisms associated with increasing IMD risk were stimulated by PAHs. The composition of PMCs differed between the three urban categories which can be largely explained by the variation of phyllosphere PAH concentration and the surrounding land-use types. Similar to our previous study, suburban areas were linked with the most potential adverse health effects, where we observed the lowest bacterial diversity, the highest relative abundance of IMD-associated bacteria, and the highest relative abundance of Pathotroph. Urban green-blue infrastructure (GBI) was positively correlated with the diversity of PMCs, whereas urban grey infrastructure tended to homogenize PMCs. Notably, GBI also reduced the relative abundance of IMD-associated and pathogenic microbes, indicating the potential health benefits of GBI in land-use planning. Taken together, our study emphasizes the need to further investigate environmental communities in contaminated traffic environments, as human microbiomes are directly exposed to risky microorganisms.

Phosphorus elevation erodes ectomycorrhizal community diversity and induces divergence of saprophytic community composition between vegetation types.

Phosphorus (P) is a critical macronutrient that is essential for many life-sustaining processes. Despite decades of work on plant performance under P deficiency and the importance of microbes in ecosystem processes, little is known about how bacterial and fungal flora respond to P gradients and determine the vegetation health. In current study, we examined soil edaphic conditions and microbial communities in 39 untouched natural forests representing phosphorous deficient (Pp) and phosphorus rich (Pr) soils (due to naturally occurring phosphate rocks) in Yunnan Province, China. We also considered the effect of plant functional types by including the dominant tree species. Bacterial and fungal diversity was greater across the Pp sites compared with Pr sites. The relative abundance of Actinobacteria and Gemmatimonadetes was higher across Pp sites, while Chlamydiae and Verrucomicrobia showed the opposite pattern, with greater relative abundance across the Pr sites. Bacterial taxa that were observed in low P soils were more likely having oligotrophic life history strategies. Interestingly, ectomycorrhizal (ECM) fungal diversity was promoted in the Pp sites, indicating that the decreasing soil P concentration and the increasing host P demand foster stimulated the ECM species for hyphal soil exploration. Moreover, the high P level caused saprophytic fungi (SAP) to diverge, causing its enrichment only under Q. variabilis compared to low P soil, where there is no difference in relative abundance of SAP between the two tree species. This likely resulted in an enhanced decomposition process by SAP and elevation of soil properties (Carbon and Nitrogen) under Q. variabilis across the Pr sites. Taken together, our findings highlight the highly diverse microbiome in low P soils. The higher soil P caused shifts of fungal functional guilds, which likely influence tree growth and health (ECM), along with divergence of ecosystem services between tree functional types.

Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable (Martes zibellina) Guts.

In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.

Fluorescent aptasensor for carbendazim detection in aqueous samples based on gold nanoparticles quenching Rhodamine B.

This paper proposes a fluorescent aptasensor for the detection of carbendazim (CBZ) in aqueous solution using CBZ-specific aptamer as sensing probe, gold nanoparticles (AuNPs) and Rhodamine B (RhoB) as indicator, respectively. In the absence of CBZ, CBZ aptamer could wrap AuNPs and maintained it dispersed in NaCl solution basically. Contrarily, the aptamer could specifically combine with CBZ and form a stable aptamer-CBZ complex, leaving AuNPs exposed to be aggregated by NaCl solution. The dispersed AuNPs could efficiently quench the fluorescence of RhoB, but those aggregated AuNPs have poor capability to impair the fluorescent indicator. Thus, the concentration of CBZ could be detected quantitatively through the distinction of the fluorescence intensity. This convenient fluorescent assay for CBZ had a wide linear range from 2.33 to 800 nM and a 2.33 nM limit of detection (LOD). Furthermore, it had high selectivity over pesticides, antibiotics, metal ions and other disrupting chemicals. As for application, the method could determine CBZ in water samples with recoveries in the range of 96.3-111.2%. This fluorescent aptasensor possessed great potential application for CBZ detection in actual aquatic environment.

Colorimetric determination of carbendazim based on the specific recognition of aptamer and the poly-diallyldimethylammonium chloride aggregation of gold nanoparticles.

This paper proposes the idea of establishing carbendazim (CBZ) colorimetric determination in spiked water samples by specific aptamers of unlabeled carbendazim (CBZ), gold nanoparticles (AuNPs) and cationic polymer poly-diallyldimethylammonium chloride (PDDA). In the absence of CBZ, the CBZ aptamer will react with the cationic polymer PDDA by electrostatic interaction to form a complex structure. Therefore, the gold nanoparticles will remain dispersed due to the lack of PDDA. However, when CBZ is added into the sensory system, the CBZ-specific aptamer can selectively capture CBZ to form a stable complex structure. Due to the consumption of the aptamer, PDDA is unable to interact with the aptamer and begins to induce aggregation of AuNPs, thereby causing the color of the solution to change from red to blue. Colorimetric determination of CBZ based on the specific recognition of aptamer and the PDDA-induced aggregation of AuNPs has a detection limit of 2.2 nM, a linear range (R = 0.9960) from 2.2 to 500 nM. The method has good sensitivity and specificity, and the average recovery of CBZ is 94.9-104.8% in the application of actual water samples. This colorimetric method is simple, time-saving and low requirements for equipment, therefore, it holds great potential for CBZ detection in the environmental water samples.

Fluorescent aptasensor for ofloxacin detection based on the aggregation of gold nanoparticles and its effect on quenching the fluorescence of Rhodamine B.

This paper proposes the idea of building a fluorescent biosensor for ofloxacin (OFL) determination in aqueous and milk samples by label-free OFL-specific aptamer, gold nanoparticles (AuNPs) and Rhodamine B (RB). In the absence of OFL, AuNPs are coated with OFL aptamer and maintain dispersed in the high concentration of NaCl. The dispersed AuNPs could reduce the strong fluorescence intensity of RB efficiently. By contrast, in the presence of OFL, OFL is combined with aptamer to form stable compounds, causing the aptamers separated from the surface of AuNPs, thus AuNPs would be exposed in the solution. And the aggregated AuNPs will not quench the fluorescence intensity of RB. Through the distinction of the fluorescence intensity, the concentration of OFL could be detected in aqueous and milk samples quantitatively. The convenient and specific fluorescent assay for OFL is established with a linear range (R = 0.9907) from 20 to 300 nM and a detection limit of 1.66 nM in aqueous solution, and a linear range (R = 0.9963) from 20 to 300 nM and a detection limit of 4.61 nM (1.66 µg/L) in milk samples. With the good sensitivity and selectivity, this biosensor has good application potential to detect OFL in food and environmental samples.