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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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%.

Terbium (III)-referenced N-doped carbon dots for ratiometric fluorescent sensing of mercury (II) in seafood.

A ratiometric fluorescence (FL) sensor was fabricated by coordinating 2, 6-pyridinedicarboxylic acid (DPA) sensitized Tb3+ (Tb-DPA) with NH2 and COOH on the surface of the N-doped carbon dots (N-CDs) for detecting Hg2+ in seafood. The sensor exhibited two FL emissions at 436 nm (N-CDs) as the response signal and at 543 nm (Tb-DPA) as the reference signal when excited at 290 nm. After adding Hg2+, the FL emission at 436 nm was significantly quenched and the FL emission at 543 nm was negligibly changed. The electron transfer (ET) between COO- of N-CDs and Hg2+ led to the FL quenching of N-CDs. The FL ratio (F436/F543) exhibited a good linear relationship in the Hg2+ concentrations of 1161.51 µM with a low limit of detection (LOD) of ~37 nM. The sensor presented high selectivity, satisfactory accuracy and precision toward Hg2+ in seafood with recoveries of 86.45-114.47% and RSDs of 0.20-1.92%.

Cu2+-Triggered Carbon Dots with Synchronous Response of Dual Emission for Ultrasensitive Ratiometric Fluorescence Determination of Thiophanate-Methyl Residues.

Copper ion (Cu2+)-triggered carbon dots (CDs/Cu) with dual emissions were utilized to develop a ratiometric fluorescence sensor for ultrasensitive detection of inert thiophanate-methyl (TM). TM could be recognized by CDs/Cu through π-π stacking and could chelate Cu2+ of CDs/Cu through metal ion coordination, inducing synchronous fluoresent quenching of the dual emission of CDs/Cu based on the excited state intramolecular proton transfer and the ligand-to-metal charge transfer. The fluorescence ratio of CDs/Cu (F416/F481) linearly responded in a TM concentration of 0.10-20.00 µmol/L with an ultralow limit of detection of 2.90 × 10-6 µmol/L. A synchronous response of the ratiometric sensor enhanced the specificity toward TM and presented remarkable capability of anti-interference in complex matrices. The sensor exhibited satifactory accuracy and precision for practical applications with recoveries of 88.33-101.09% and relative standard deviations of 1.61-5.06%, demonstrating an ultrasensitive ratiometric fluorescent nanosensor for detecting pesticides residues in complex matrices.

Upward elevation and northwest range shifts for alpine Meconopsis species in the Himalaya-Hengduan Mountains region.

Climate change may impact the distribution of species by shifting their ranges to higher elevations or higher latitudes. The impacts on alpine plant species may be particularly profound due to a potential lack of availability of future suitable habitat. To identify how alpine species have responded to climate change during the past century as well as to predict how they may react to possible global climate change scenarios in the future, we investigate the climatic responses of seven species of Meconopsis, a representative genus endemic in the alpine meadow and subnival region of the Himalaya-Hengduan Mountains. We analyzed past elevational shifts, as well as projected shifts in longitude, latitude, elevation, and range size using historical specimen records and species distribution modeling under optimistic (RCP 4.5) and pessimistic (RCP 8.5) scenarios across three general circulation models for 2070. Our results indicate that across all seven species, there has been an upward shift in mean elevation of 302.3 m between the pre-1970s (1922-1969) and the post-1970s (1970-2016). The model predictions suggest that the future suitable climate space will continue to shift upwards in elevation (as well as northwards and westwards) by 2070. While for most of the analyzed species, the area of suitable climate space is predicted to expand under the optimistic emission scenario, the area contracts, or, at best, shows little change under the pessimistic scenario. Species such as M. punicea, which already occupy high latitudes, are consistently predicted to experience a contraction of suitable climate space across all the models by 2070 and may consequently deserve particular attention by conservation strategies. Collectively, our results suggest that the alpine high-latitude species analyzed here have already been significantly impacted by climate change and that these trends may continue over the coming decades.

Distributional responses to climate change for alpine species of Cyananthus and Primula endemic to the Himalaya-Hengduan Mountains.

Global warming increases the vulnerability of plants, especially alpine herbaceous species, to local extinction. In this study, we collected species distribution information from herbarium specimens for ten selected Cyananthus and Primula alpine species endemic to the Himalaya-Hengduan Mountains (HHM). Combined with climate data from WorldClim, we used Maximum Entropy Modeling (MaxEnt) to project distributional changes from the current time period to 2070. Our predictions indicate that, under a wide range of climate change scenarios, the distributions of all species will shift upward in elevation and northward in latitude; furthermore, under these scenarios, species will expand the size of their range. For the majority of the species in this study, habitats are available to mitigate upward and northward shifts that are projected to be induced by changing climate. If current climate projections, however, increase in magnitude or continue to increase past our projection dates, suitable habitat for future occupation by alpine species will be limited as we predict range contraction or less range expansion for some of the species under more intensified climate scenarios. Our study not only underscores the value of herbarium source information for future climate model projections but also suggests that future studies on the effects of climate change on alpine species should include additional biotic and abiotic factors to provide greater resolution of the local dynamics associated with species persistence under a warming climate.