Adding experimental precision to the realism of field observations: Plant communities structure bacterial communities in a glacier forefield.

Ecological studies are aligned along a realism-precision continuum ranging from field observations to controlled lab experiments that each have their own strengths and limitations. Ecological insight may be most robust when combining approaches. In field observations along a successional gradient, we found correlations between plant species composition and soil bacterial communities, while bacterial Shannon diversity was unrelated to vegetation characteristics. To add a causal understanding of the processes of bacterial community assembly, we designed lab experiments to specifically test the influence of plant composition on bacterial communities. Using soil and seeds from our field site, we added different combinations of surface-sterilised seeds to homogenised soil samples in microcosms and analysed bacterial communities 4 months later. Our results confirmed the field observations suggesting that experimental plant community composition shaped bacterial community composition, while Shannon diversity was unaffected. These results reflect intimate plant-bacteria interactions that are important drivers of plant health and community assembly. While this study provided insights into the role of plants underlying the assembly of bacterial communities, we did not experimentally manipulate other drivers of community assembly such as abiotic factors. Therefore, we recommend multi-factorial laboratory experiments to quantify the relative importance of different factors contributing to microbial composition.

Tailored Monoacyl Poly(2-oxazoline)- and Poly(2-oxazine)-Lipids as PEG-Lipid Alternatives for Stabilization and Delivery of mRNA-Lipid Nanoparticles.

The successful use of lipid nanoparticles (LNPs) for clinical development of the COVID-19 mRNA vaccines marked a breakthrough in mRNA-LNP therapeutics. As one of the vital components of LNPs, poly(ethylene glycol)-lipid conjugates (PEG-lipids) influence particle biophysical properties and stability, as well as interactions within biological environments. Reports suggesting that anti-PEG antibodies can be detected quite commonly within the human population raise concerns that PEG content in commercial LNP products could further stimulate immune responses to PEG. The presence of anti-PEG antibodies has been linked to accelerated clearance of LNPs, potentially a source of variability in the biological response to mRNA-LNP products. This motivated us to explore potential PEG alternatives. Herein, we report physicochemical and biological properties of mRNA-LNPs assembled using poly(2-oxazoline) (POx)- and poly(2-oxazine) (POz)-based polymer-lipid conjugates. Notably, we investigated monoacyl lipids as alternatives to diacyl lipids. mRNA-LNPs produced using monoacyl POx/POz-lipids displayed comparable biophysical characteristics and cytocompatibility. Delivery of reporter mRNA resulted in similar transfection efficiencies, in both adherent and suspension cells, and in mice, compared to PEG-lipid equivalents. Our results suggest that monoacyl POx/POz-lipid-containing LNPs are promising candidates for the development of PEG-free LNP-based therapeutic products.

Carbon dots based ratiometric fluorescent sensing platform for food safety.

Food safety has become a major global concern and the rapid detection of food nutritional ingredients and contaminants has aroused much more attention. Nanomaterials-based fluorescent sensing holds great potential in designing highly sensitive and selective detection strategies for food safety analysis. Carbon dots (CDs) possess tremendous prospects in fluorescent sensing food ingredients and contaminants due to their superior properties of chemical and photostability, highly fluorescence with tunability, and no/low-toxicity. Numerous endeavors are demanded to contribute to overcoming the challenge of lower sensitivity and selectivity of the sensors interfered by various components in intricate food matrices to ensure food safety and human health. Nanohybrid CDs based ratiometric fluorescent sensing with self-calibration is regarded as an efficient strategy for the CDs based sensors for the specific recognition of target analyte in the food matrices. This work is devoted to reviewing the development of nanohybrid CDs based ratiometric fluorescent sensing platform and the perspectives of the platform for food safety. The applications of nanohybrid CDs in sensing are summarized and the sensing mechanisms are briefly discussed.

Visible-blind and flexible metal-semiconductor-metal ultraviolet photodetectors based on sub-10-nm thick silver interdigital electrodes.

We propose and experimentally demonstrate a distinct visible-blind and flexible metal-semiconductor-metal ultraviolet (UV) photodetector (PD) based on sub-10-nm thick silver interdigital electrodes. The transparent PD with 7-nm thick electrodes shows enhanced visible transmittance (80%) in average and achieves greatly improved responsivity (60.5 mA/W), and detectivity (1.75×1010 Jones) at 5 V under 380-nm illumination, compared with its opaque counterpart. It is as fast as the opaque PD with short rise and fall times (22.4 and 11.5 ms) and shows good flexibility. All the properties are comparable or superior to many reported transparent UV PDs, mainly attributed to the broad high UV-visible transmittance and the high conductivity of the ultrathin silver film.

Reconfigurable RGB dye lasers based on the laminar flow control in an optofluidic chip.

The optofluidic dye laser serves as an important on-chip optical source in microfluidic technology for a breadth of applications. One of the ultimate goals of such a light source is an optofluidic white dye laser. However, realizing such a device has been challenging, because it is difficult to achieve simultaneous multi-wavelength lasers that span the most visible spectrum, especially on an integrated system. Here, we demonstrate white lasing in an optofluidic chip that simultaneously lases in red, green, and blue (RGB) colors inside a microfluidic channel. A Fabry-Perot cavity formed by two end-coated fibers provides the optical feedback of the laser. Easy reconfigurable emission can be obtained based on the laminar flow control. Eventually, white lasing at a low threshold was obtained when the pumping energy density is in excess of 26.1 µJ/mm2.

Electro-optic phase modulation with a symmetrical metal-cladding waveguide.

A bulk electro-optic (EO) modulator based on the ultrahigh-order guided modes, which are excited in a symmetrical metal-cladding waveguide (SMCW), has been exploited. This kind of mode in a SMCW has high sensitivity to phase shift by changing the refractive index of the guiding layer. Compared with phase modulation via the bulk EO modulator without a waveguide, the applied half-wave voltage is reduced for one magnitude. This work may have practical applications in optical information processes.

Decrease in expression of maternal effect gene Mater is associated with maternal ageing in mice.

STUDY HYPOTHESIS: What factors in mouse oocytes are involved in the ageing-related decline in oocyte quality? STUDY FINDING: The maternal effect gene Mater is involved in ageing-related oocyte quality decline in mice. WHAT IS KNOWN ALREADY: Premature loss of centromere cohesion is a hallmark of ageing-related oocyte quality decline; the maternal effect gene Mater (maternal antigen that embryos require, also known as Nlrp5) is required for preimplantation embryo development beyond the 2-cell stage, and mRNA expression of Mater decreases with maternal ageing. STUDY DESIGN, SAMPLES/MATERIALS, METHODS: Mater protein expression level in mature oocytes from 7 young (5-8 weeks old) to 7 old mice (41-68 weeks old) was compared by immunoblotting analysis. Wild-type and Mater-null mice were used to examine whether Mater is necessary for maintaining normal centromere cohesion by means of cytogenetic karyotyping, time-lapse confocal microscopy and immunofluorescence staining. MAIN RESULTS AND THE ROLE OF CHANCE: Mater protein is decreased in mature oocytes from old versus young mice (P = 0.0022). Depletion of Mater from oocytes leads to a reduction in centromere cohesion, manifested by precocious sister chromatid separation, enlargement of sister centromere distance and misalignment of chromosomes in the metaphase plate during meiosis I and II. LIMITATIONS, REASONS FOR CAUTION: This study was conducted in mice. Whether or not the results are applicable to human remains further elucidation. In addition, we were unable to confirm if the strain of mice (C57BL/6XSv129) at the age of 41-68 weeks old has the 'cohesin-loss' phenotype. WIDER IMPLICATIONS OF THE FINDINGS: Investigating Mater's functional mechanisms could provide fresh insights into understanding how the ageing-related oocyte quality decline occurs. LARGE SCALE DATA: N/A. STUDY FUNDING AND COMPETING INTERESTS: This work was supported by the research grant from Chinese NSFC to P.Z. (31071274). We have no conflict of interests to declare.

Sequential stacking link prediction algorithms for temporal networks.

Link prediction algorithms are indispensable tools in many scientific applications by speeding up network data collection and imputing missing connections. However, in many systems, links change over time and it remains unclear how to optimally exploit such temporal information for link predictions in such networks. Here, we show that many temporal topological features, in addition to having high computational cost, are less accurate in temporal link prediction than sequentially stacked static network features. This sequential stacking link prediction method uses 41 static network features that avoid detailed feature engineering choices and is capable of learning a highly accurate predictive distribution of future connections from historical data. We demonstrate that this algorithm works well for both partially observed and completely unobserved target layers, and on two temporal stochastic block models achieves near-oracle-level performance when combined with other single predictor methods as an ensemble learning method. Finally, we empirically illustrate that stacking multiple predictive methods together further improves performance on 19 real-world temporal networks from different domains.

Link prediction accuracy on real-world networks under non-uniform missing-edge patterns.

Real-world network datasets are typically obtained in ways that fail to capture all edges. The patterns of missing data are often non-uniform as they reflect biases and other shortcomings of different data collection methods. Nevertheless, uniform missing data is a common assumption made when no additional information is available about the underlying missing-edge pattern, and link prediction methods are frequently tested against uniformly missing edges. To investigate the impact of different missing-edge patterns on link prediction accuracy, we employ 9 link prediction algorithms from 4 different families to analyze 20 different missing-edge patterns that we categorize into 5 groups. Our comparative simulation study, spanning 250 real-world network datasets from 6 different domains, provides a detailed picture of the significant variations in the performance of different link prediction algorithms in these different settings. With this study, we aim to provide a guide for future researchers to help them select a link prediction algorithm that is well suited to their sampled network data, considering the data collection process and application domain.

Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast.

Phytoalexin sakuranetin functions in resistance against rice blast. However, the mechanisms underlying the effects of sakuranetin remains elusive. Here, we report that rice lines expressing resistance (R) genes were found to contain high levels of sakuranetin, which correlates with attenuated endocytic trafficking of plasma membrane (PM) proteins. Exogenous and endogenous sakuranetin attenuates the endocytosis of various PM proteins and the fungal effector PWL2. Moreover, accumulation of the avirulence protein AvrCO39, resulting from uptake into rice cells by Magnaporthe oryzae, was reduced following treatment with sakuranetin. Pharmacological manipulation of clathrin-mediated endocytic (CME) suggests that this pathway is targeted by sakuranetin. Indeed, attenuation of CME by sakuranetin is sufficient to convey resistance against rice blast. Our data reveals a mechanism of rice against M. oryzae by increasing sakuranetin levels and repressing the CME of pathogen effectors, which is distinct from the action of many R genes that mainly function by modulating transcription.

Ecological network analysis reveals cancer-dependent chaperone-client interaction structure and robustness.

Cancer cells alter the expression levels of metabolic enzymes to fuel proliferation. The mitochondrion is a central hub of metabolic reprogramming, where chaperones service hundreds of clients, forming chaperone-client interaction networks. How network structure affects its robustness to chaperone targeting is key to developing cancer-specific drug therapy. However, few studies have assessed how structure and robustness vary across different cancer tissues. Here, using ecological network analysis, we reveal a non-random, hierarchical pattern whereby the cancer type modulates the chaperones' ability to realize their potential client interactions. Despite the low similarity between the chaperone-client interaction networks, we highly accurately predict links in one cancer type based on another. Moreover, we identify groups of chaperones that interact with similar clients. Simulations of network robustness show that this group structure affects cancer-specific response to chaperone removal. Our results open the door for new hypotheses regarding the ecology and evolution of chaperone-client interaction networks and can inform cancer-specific drug development strategies.

Microbiota alteration of Chinese young male adults with high-status negative cognitive processing bias.

Introduction: Evidence suggests that negative cognitive processing bias (NCPB) is a significant risk factor for depression. The microbiota-gut-brain axis has been proven to be a contributing factor to cognitive health and disease. However, the connection between microbiota and NCPB remains unknown. This study mainly sought to explore the key microbiota involved in NCPB and the possible pathways through which NCPB affects depressive symptoms. Methods: Data in our studies were collected from 735 Chinese young adults through a cross-sectional survey. Fecal samples were collected from 35 young adults with different levels of NCPB (18 individuals were recruited as the high-status NCPB group, and another 17 individuals were matched as the low-status NCPB group) and 60 with different degrees of depressive symptoms (27 individuals were recruited into the depressive symptom group, as D group, and 33 individuals were matched into the control group, as C group) and analyzed by the 16S ribosomal RNA sequencing technique. Results: As a result, the level of NCPB correlated with the degree of depressive symptoms as well as anxiety symptoms and sleep quality (p < 0.01). The ß-diversity of microbiota in young adults was proven to be significantly different between the high-status NCPB and the low-status NCPB groups. There were several significantly increased bacteria taxa, including Dorea, Christensenellaceae, Christe -senellaceae_R_7_group, Ruminococcaceae_NK4A214_group, Eggerthellaceae, Family-XIII, Family_XIII_AD3011_group, Faecalibaculum, and Oscillibacter. They were mainly involved in pathways including short-chain fatty acid (SCFA) metabolism. Among these variable bacteria taxa, Faecalibaculum was found associated with both NCPB and depressive symptoms. Furthermore, five pathways turned out to be significantly altered in both the high-status NCPB group and the depressive symptom group, including butanoate metabolism, glyoxylate and dicarboxylate metabolism, propanoate metabolism, phenylalanine, tyrosine, and tryptophan biosynthesis, valine, leucine, and isoleucine degradation. These pathways were related to SCFA metabolism. Discussion: Fecal microbiota is altered in Chinese young male adults with high status NCPB and may be involved in the biochemical progress that influences depressive symptoms.

Exploring the Frequency and Distribution of Ecological Non-monotonicity in Associations among Ecosystem Constituents.

Complex links between biotic and abiotic constituents are fundamental for the functioning of ecosystems. Although non-monotonic interactions and associations are known to increase the stability, diversity, and productivity of ecosystems, they are frequently ignored by community-level standard statistical approaches. Using the copula-based dependence measure qad, capable of quantifying the directed and asymmetric dependence between variables for all forms of (functional) relationships, we determined the proportion of non-monotonic associations between different constituents of an ecosystem (plants, bacteria, fungi, and environmental parameters). Here, we show that up to 59% of all statistically significant associations are non-monotonic. Further, we show that pairwise associations between plants, bacteria, fungi, and environmental parameters are specifically characterized by their strength and degree of monotonicity, for example, microbe-microbe associations are on average stronger than and differ in degree of non-monotonicity from plant-microbe associations. Considering directed and non-monotonic associations, we extended the concept of ecosystem coupling providing more complete insights into the internal order of ecosystems. Our results emphasize the importance of ecological non-monotonicity in characterizing and understanding ecosystem patterns and processes. Supplementary Information: The online version contains supplementary material available at 10.1007/s10021-023-00867-9.

Succession comprises a sequence of threshold-induced community assembly processes towards multidiversity.

Research on successions and community assembly both address the same processes such as dispersal, species sorting, and biotic interactions but lack unifying concepts. Recent theoretical advances integrated both research lines proposing a sequence of stochastic and deterministic processes along successional gradients. Shifts in ecosystem states along successional gradients are predicted to occur abruptly once abiotic and biotic factors dominate over dispersal as main driver. Considering the multidiversity composed of five organismal groups including plants, animals, and microbes, our results imply that stochastic, likely dispersal-dominated, processes are replaced by rather deterministic processes such as environmental filtering and biotic interactions after around 60 years of succession in a glacier forefield. The niche-based character of later successional processes is further supported by a decline in multi-beta-diversity. Our results may update concepts of community assembly by considering multiple taxa, help to bridge the gap between research on successions and community assembly, and provide insights into the emergence of multidiverse and complex ecosystems.

Accuracy of mutual predictions of plant and microbial communities vary along a successional gradient in an alpine glacier forefield.

Receding glaciers create virtually uninhabited substrates waiting for initial colonization of bacteria, fungi and plants. These glacier forefields serve as an ideal ecosystem for studying transformations in community composition and diversity over time and the interactions between taxonomic groups in a dynamic landscape. In this study, we investigated the relationships between the composition and diversity of bacteria, fungi, and plant communities as well as environmental factors along a successional gradient. We used random forest analysis assessing how well the composition and diversity of taxonomic groups and environmental factors mutually predict each other. We did not identify a single best indicator for all taxonomic and environmental properties, but found specific predictors to be most accurate for each taxon and environmental factor. The accuracy of prediction varied considerably along the successional gradient, highlighting the dynamic environmental conditions along the successional gradient that may also affect biotic interactions across taxa. This was also reflected by the high accuracy of predictions of plot age by all taxa. Next to plot age, our results indicate a strong importance of pH and temperature in structuring microbial and plant community composition. In addition, taxonomic groups predicted the community composition of each other more accurately than environmental factors, which may either suggest that these groups similarly respond to other not measured environmental factors or that direct interactions between taxa shape the composition of their communities. In contrast, diversity of taxa was not well predicted, suggesting that community composition of one taxonomic group is not a strong driver of the diversity of another group. Our study provides insights into the successional development of multidiverse communities shaped by complex interactions between taxonomic groups and the environment.

A susceptible multifunctional fluorescent probe based on levulinic acid for the practical detection of SO2.

Sulfites (HSO3-) are used as preservatives and additives in many foods and medicines. However, a high sulfite concentration can cause asthma attacks and even breathing difficulties. Sulfites can also accumulate from the environment into the body, so it is necessary to develop a probe capable of detecting SO2 in the environment and in organisms. A multifunctional sensor, SO-2, based on levulinic acid was designed and synthesized. SO-2 showed an excellent response to SO2 with a detection limit of 2.0 × 10-8 M and a fast response equilibrium time (within 10 min), which indicated that the probe could detect SO2 with high sensitivity. The probe also successfully traced exogenous bisulfite in cells and was applied to analyze water samples in a natural environment.

Characteristics of members of IGT family genes in controlling rice root system architecture and tiller development.

Root system architecture (RSA) and tiller are important agronomic traits. However, the mechanisms of the IGT family genes regulate RSA and tiller development in different rice varieties remain unclear. In this study, we demonstrated that 38 rice varieties obtained from Yuanyang Hani's terraced fields with different RSA and could be classified into six groups based on the ratio of root length and width. We found a positive correlation between RSA (including root width, length, and area) and tiller number in most of rice varieties. Furthermore, the IGT family genes Deeper Rooting 1 (DRO1), LAZY1, TAC1, and qSOR1 showed different expression patterns when rice grown under irrigation and drought conditions. Moreover, the qSOR1 gene had higher levels in the roots and tillers, and accompanied with higher levels of PIN1b gene in roots when rice grown under drought environmental condition. DRO1 gene had two single nucleotide polymorphisms (SNPs) in the exon 3 sequences and showed different expression patterns in the roots and tillers of the 38 rice varieties. Overexpression of DRO1 with a deletion of exon 5 caused shorter root length, less lateral roots and lower levels of LAZY1, TAC1, and qSOR1. Further protein interaction network, microRNA targeting and co-expression analysis showed that DRO1 plays a critical role in the root and tiller development associated with auxin transport. These data suggest that the RSA and tiller development are regulated by the IGT family genes in an intricate network way, which is tightly related to rice genetic background in rice adapting to different environmental conditions.

Patterned few nanometer-thick silver films with high optical transparency and high electrical conductivity.

Transparent conductive electrodes (TCEs) are experimentally demonstrated using patterned few nanometer-thick silver films on zinc oxide-coated rigid and flexible substrates. The grid lines are completely continuous, but only 8.4 nm thick. This is the thinnest metallic grid we are aware of. Owing to the high transparency of both the grid lines and spacing, our TCE with an opening ratio (OR) as small as 36% achieves an average optical transmittance up to ∼90% in the visible regime, breaking the optical limits of both the unpatterned film counterpart and the thick grid counterpart (whose optical transmittance is determined by the OR). The small OR enables a low sheet resistance of ∼21.5 Ω sq-1. The figure of merit up to ∼17 kΩ-1 is superior to those of the unpatterned film counterpart, our fabricated 180 nm thick ITO, as well as most reported thick metal grid TCEs. Our ultrathin TCE, firmly attached to the substrate, is mechanically more flexible and more stable than the film counterpart and ITO. As a flexible transparent film heater, it achieves comparable or even superior heating performances with previously-reported heaters and performs well in a thermochromic test.

Divergent assembly processes? A comparison of the plant and soil microbiome with plant communities in a glacier forefield.

Community assembly is a result of dispersal, abiotic and biotic characteristics of the habitat as well as stochasticity. A direct comparison between the assembly of microbial and 'macrobial' organisms is hampered by the sampling of these communities in different studies, at different sites or on different scales. In a glacier forefield in the Austrian Alps, we recorded the soil and plant microbiome (bacteria and fungi) and plants that occurred in the same landscape and in close proximity in the same plots. We tested five predictions deduced from assembly processes and revealed deviating patterns of assembly in these community types. In short, microbes appeared to be less dispersal limited than plants and soil microbes, and plants strongly responded to abiotic factors whereas the leaf microbiome was plant species specific and well buffered from environmental conditions. The observed differences in community assembly processes may be attributed to the organisms' dispersal abilities, the exposure of the habitats to airborne propagules and habitat characteristics. The finding that assembly is conditional to the characteristics of the organisms, the habitat and the spatial scale under consideration is thus central for our understanding about the establishment and the maintenance of biodiversity.

Ratiometric fluorescent sensing carbendazim in fruits and vegetables via its innate fluorescence coupling with UiO-67.

A ratiometric fluorescent sensor was facilely fabricated using innate fluorescence of carbendazim (MBC) and fluorescent UiO-67 to sensitively and selectively detect MBC in food matrixes. The innate fluorescence of MBC provided a signal at 311 nm (F311), and the fluorescent UiO-67 at 408 nm (F408) could recognize MBC through π-π stacking inducing fluorescent quenching relied on photoelectron transfer (PET). The ratio (F311/F408) of the fluorescence enhancement of MBC and the quenching of UiO-67 linearly responded to the MBC concentrations of 0-47.6 µmol/L with a low limit of detection (LOD) of 3.0 × 10-3 µmol/L. The reverse response signals of the sensor enhanced the sensitivity toward MBC and presented remarkable anti-interference capability in complex matrices. The as-prepared sensor was applied to detect MBC residues in apple, cucumber and cabbage, obtaining satisfactory accuracy and precision with the recovery of 90.82-103.45% and RSDs of lower than 3.03%.