One-Shot Single-Cell Proteome and Metabolome Analysis Strategy for the Same Single Cell.

Characterizing the profiles of proteome and metabolome at the single-cell level is of great significance in single-cell multiomic studies. Herein, we proposed a novel strategy called one-shot single-cell proteome and metabolome analysis (scPMA) to acquire the proteome and metabolome information in a single-cell individual in one injection of LC-MS/MS analysis. Based on the scPMA strategy, a total workflow was developed to achieve the single-cell capture, nanoliter-scale sample pretreatment, one-shot LC injection and separation of the enzyme-digested peptides and metabolites, and dual-zone MS/MS detection for proteome and metabolome profiling. Benefiting from the scPMA strategy, we realized dual-omic analysis of single tumor cells, including A549, HeLa, and HepG2 cells with 816, 578, and 293 protein groups and 72, 91, and 148 metabolites quantified on average. A single-cell perspective experiment for investigating the doxorubicin-induced antitumor effects in both the proteome and metabolome aspects was also performed.

Fe3O4-doped silk fibroin-polyacrylamide hydrogel for selective and highly efficient absorption of cationic dyes pollution in water.

Overuse of organic dyes has caused serious threats to the ecosystem and human health. However, the development of high-efficient, environmentally friendly, selective, and degradable cationic dye adsorbents remains a huge challenge. In this work, a novel Fe3O4nanoparticles doped silk fibroin-polyacrylamide magnetic hybrid hydrogel (Fe3O4@SF-PAAM) was successfully fabricated by combining free radical polymerization to prepare hydrogels andin situco-precipitation to prepare nanoparticles. The obtained Fe3O4@SF-PAAM hydrogel shows strong magnetic performance with saturated magnetic of 10.2 emu mg-1and excellent swelling properties with a swelling ratio of 55867%. In addition, Fe3O4@SF-PAAM can adsorb cationic dyes such as methylene blue (MB), crystal violet, and Rhodamine B, but has no adsorption effect on anionic dyes such as methyl orange, congo red, and carmine, indicating that Fe3O4@SF-PAAM has good selective adsorption properties for cationic dyes. Interestingly, the adsorption capacity of Fe3O4@SF-PAAM was approached 2025 mg g-1for MB (MB, a typical cation dye) at 25 °C and neutral. Meanwhile, the hybrid hydrogel is reusable, the removal rate for MB is still over 90% after the five adsorption-desorption cycles. The fabricated magnetic hybrid hydrogel is a kind of a highly-efficiency and eco-friendly adsorbent and presents great potential applications in water purification and environmental protection.

Manganese(II)-doped zinc/germanium oxide nanoparticles as a viable fluorescent probe for visual and time-resolved fluorometric determination of ascorbic acid and its oxidase.

A method is described for the determination of ascorbic acid (AA) in complex biological fluids. It based on maganese(II)-doped zinc/germanium oxide nanoparticles (Mn@ZnGe NPs) with appealing time-resolved phosphorescence (TRP). TRP can provide a background-free reporter signal in analytical methods. The absorption of AA overlaps the excitation band of Mn@ZnGe NPs at 254 nm. This reduces the intensity of fluorescence via an inner filter effect (IFE) with increasing concentration of AA. Typical experimental conditions include an emission peak at 536 nm, a delay time of 50 µs and a counting time of 2 ms. This method can detect AA in a range of 5-500 µM with a 0.13 µM limit of detection. If AA is oxidized by the enzyme AA oxidase (AAOx), dehydroascorbic acid will be formed which doesn't absorb at 254 nm. Hence, the IFE cannot occur and fluorescence is not reduced. The strategy can be used to quantify AAOx in the activity range of 1-4 U·mL-1. By using a handheld UV lamp and a smart phone with a color-scanning feature, the feasibility for visual detection and real-time/onsite quantitative scanometric monitoring of AA and AAOx is demonstrated. Graphical abstract Schematic presentation of a fluorometric method for determination of ascorbic acid (AA) and ascorbic oxidase and a scanometric visual assay. It based on the use of maganese(II)-doped zinc/germanium oxide nanoparticles (Mn@ZnGe NPs) with appealing time-resolved phosphorescence (TRP) and the inner-filter effect (IFE) between AA and Mn@ZnGe NPs.

Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a Mammalian cell.

The shotgun proteomic analysis is currently the most promising single-cell protein sequencing technology, however its identification level of ~1000 proteins per cell is still insufficient for practical applications. Here, we develop a pick-up single-cell proteomic analysis (PiSPA) workflow to achieve a deep identification capable of quantifying up to 3000 protein groups in a mammalian cell using the label-free quantitative method. The PiSPA workflow is specially established for single-cell samples mainly based on a nanoliter-scale microfluidic liquid handling robot, capable of achieving single-cell capture, pretreatment and injection under the pick-up operation strategy. Using this customized workflow with remarkable improvement in protein identification, 2449-3500, 2278-3257 and 1621-2904 protein groups are quantified in single A549 cells (n = 37), HeLa cells (n = 44) and U2OS cells (n = 27) under the DIA (MBR) mode, respectively. Benefiting from the flexible cell picking-up ability, we study HeLa cell migration at the single cell proteome level, demonstrating the potential in practical biological research from single-cell insight.

Simultaneous deep transcriptome and proteome profiling in a single mouse oocyte.

Although single-cell multi-omics technologies are undergoing rapid development, simultaneous transcriptome and proteome analysis of a single-cell individual still faces great challenges. Here, we developed a single-cell simultaneous transcriptome and proteome (scSTAP) analysis platform based on microfluidics, high-throughput sequencing, and mass spectrometry technology to achieve deep and joint quantitative analysis of transcriptome and proteome at the single-cell level, providing an important resource for understanding the relationship between transcription and translation in cells. This platform was applied to analyze single mouse oocytes at different meiotic maturation stages, reaching an average quantification depth of 19,948 genes and 2,663 protein groups in single mouse oocytes. In particular, we analyzed the correlation of individual RNA and protein pairs, as well as the meiosis regulatory network with unprecedented depth, and identified 30 transcript-protein pairs as specific oocyte maturational signatures, which could be productive for exploring transcriptional and translational regulatory features during oocyte meiosis.

Mate Choice in Double-Breeding Female Great Tits (Parus Major): Good Males or Compatible Males.

Producing two broods within the same season may be a good strategy by which short-lived species can maximize reproductive success. To produce two clutches in the same breeding season and to ensure offspring quality, choosing a good mate is important for females. Previous studies on double breeding focused on the associated influencing factors, and few studies examined how females choose social mates. Good genes and genetic compatibility are the two main hypotheses of the genetic benefit that females obtain from choosing mates. Uncovering the method used in mate choice for genetic benefits adopted by double-breeding females would provide a better understanding of the life history and rules of female choice. The great tit is an optionally double-breeding species in temperate-latitude populations. Here, we used a dataset for a Chinese population monitored between 2014 and 2016 to test two hypotheses on double-breeding female mate choice. A total of 30.1% of the breeding pairs initiated second breeding attempts, always remating with the same mate. The date of the first egg of the first brood did not affect initiation of a second brood, and female individual heterozygosity slightly influenced initiation of a second breeding. Female great tits choose males with both compatible genes and good genes in double-breeding mating. Double-breeding females prefer males with large breast stripes, high heterozygosity, and lower relatedness, while tarsus length, repertoire size, and individual F are not the main factors considered by females when selecting males for double breeding. The number of offspring of the first clutch did not affect the pairing status of male great tits in double breeding. The genetic quality of offspring from double-breeding pairs was higher than that of those from single-breeding pairs (higher heterozygosity and lower individual F). Taken together, our results showed that double breeding female great tits adopt multiple methods for genetic benefits to choose mates.

Coordination polymers of Tb3+/Nucleotide as smart chemical nose/tongue toward pattern-recognition-based and time-resolved fluorescence sensing.

The abundant functional groups on guanosine monophosphate (GMP) make it possible to interact with various metal ions. The subtle difference in the structure of GMP and deoxy-guanosine monophosphate (dGMP) coupled with Tb3+ can be readily exploited to form two coordination polymers, which have been unveiled as two time-resolved fluorescence (TRF) sensing reporters (Tb-GMP and Tb-dGMP) in our study. Based on this finding, herein, we have proposed a novel TRF orthogonal sensing array (Tb-GMP/dGMP) for pattern-recognition-based sensing of various metal ions. In addition, upon integration of some thiol-affinity metal ions, Tb-GMP/dGMP can be further extended to construct two metal ion-involved pattern-recognition-based sensor arrays (Tb-GMP/dGMP-Cu, Tb-GMP/dGMP-Ag) for the TRF sensing different levels of disease-relevant biothiols in biofluids, illustrating the powerful and multifunctional capabilities of the Tb-GMP/dGMP system and would inspire simpler and more widespread designs of chemical nose/tongue-based applications.

Inorganic-Organic Hybrid Tongue-Mimic for Time-Resolved Luminescent Noninvasive Pattern and Chiral Recognition of Thiols in Biofluids toward Healthcare Monitoring.

In this work, manganese(II)-doped zinc/germanium oxide nanoparticles (Mn@ZGNPs) have been hydrothermally synthesized to equip with appealing time-resolved luminescence (TRL). Interestingly, we reveal that they can be readily quenched ("turn off") via a facile surface coating with bioinspired polydopamine (PDA) polymerized from dopamine (DA), resulting from PDA-triggered TRL resonance energy transfer (TRL-RET). By integrated with the thiol-induced inhibition of PDA formation, an ingenious inorganic-organic hybrid tongue-mimic sensor array is thus unveiled for noninvasive pattern recognition of thiols in biofluids in a TRL-RET-reversed "turn on" format toward healthcare monitoring. The sensing principle is based on the new finding that there are differential inhibitions from thiols against the polymerization of DA with various concentrations. Furthermore, density function theory (DFT) studies excellently prove our sensing principle and experimental results, reinforcing the power of the presented system. More importantly, chiral recognition of varied concentrations and mixtures of cysteine enantiomers using our platform are also been demonstrated, promising its practical usage. This is a novel concept of inorganic-organic hybrid-based pattern and chiral recognition platform for TRL background-free sensing and would sprout more novel relevant strategies toward broader applications.

Low level of extra-pair paternity between nearest neighbors results from female preference for high-quality males in the yellow-rumped flycatcher (Ficedula zanthopygia).

Extra-pair copulation is considered to be a means by which females can modify their initial mate choice, and females might obtain indirect benefits to offspring fitness by engaging in this behavior. Here, we examined the patterns of extra-pair paternity and female preferences in the yellow-rumped flycatcher (Ficedula zanthopygia). We found that female yellow-rumped flycatchers are more likely to choose larger and relatively highly heterozygous males than their social mates as extra-pair mates, that the genetic similarity of pairs that produced mixed-paternity offspring did not differ from the similarity of pairs producing only within-pair offspring, and that extra-pair offspring were more heterozygous than their half-siblings. These findings support the good genes hypothesis but do not exclude the compatibility hypothesis. Most female yellow-rumped flycatchers attained extra-pair paternity with distant males rather than their nearest accessible neighboring males, and no differences in genetic and phenotypic characteristics were detected between cuckolded males and their nearest neighbors. There was no evidence that extra-pair mating by female flycatchers reduced inbreeding. Moreover, breeding density, breeding synchrony and their interaction did not affect the occurrence of extra-pair paternity in this species. Our results suggest that the variation in extra-pair paternity distribution between nearest neighbors in some passerine species might result from female preference for highly heterozygous males.