The impact of mixed planting of Poaceae species in the Qinghai-Tibet plateau region on forage yield, soil nutrients, and soil microbial communities.

Establishing cultivated grassland in the Qinghai-Tibet Plateau region is an effective method to address the conflict between vegetation and livestock. However, the high altitude, low temperature, and arid climate in the region result in slow regeneration and susceptibility to degradation of mixed cultivation grassland containing perennial legumes and gramineous plants. Therefore, we aim to through field experiments, explore the feasibility of establishing mixed cultivation grassland of Poaceae species in the region by utilizing two grass species, Poa pratensis L. and Puccinellia tenuiflora. By employing a mixture of P. pratensis and P. tenuiflora to establish cultivated grassland, we observed significant changes in forage yield over time. Specifically, during the 3rd to 6th years of cultivation, the yield in the mixed grassland was higher than in monocultures. It exceeded the yield of monoculture P. tenuiflora by 19.38% to 29.14% and surpassed the monoculture of P. pratensis by 17.18% to 62.98%. Through the analysis of soil physicochemical properties and soil microbial communities in the cultivated grassland, the study suggests that the mixed grassland with Poaceae species can enhance soil enzyme activity and improve soil microbial communities. Consequently, this leads to increased soil nutrient levels, enhanced nitrogen fixation efficiency, and improved organic phosphorus conversion efficiency. Therefore, establishing mixed grasslands with Poaceae species in the Qinghai-Tibet Plateau region is deemed feasible.

Maternal PFOS exposure affects offspring development in Nrf2-dependent and independent ways in zebrafish (Danio rerio).

Perfluorooctanesulfonic acid (PFOS) is a ubiquitous legacy environmental contaminant detected broadly in human samples and water supplies. PFOS can cross the placenta and has been detected in cord blood and breastmilk samples, underscoring the importance of understanding the impacts of maternal PFOS exposure during early development. This study aimed to investigate the effects of a preconception exposure to PFOS on developmental endpoints in offspring, as well as examine the role of the transcription factor Nuclear factor erythroid-2-related factor (Nrf2a) in mediating these effects. This transcription factor regulates the expression of several genes that protect cells against oxidative stress including during embryonic development. Adult female zebrafish were exposed to 0.02, 0.08 or 0.14 mg/L PFOS for 1 week (duration of one cycle of oocyte maturation) and then paired with unexposed males from Nrf2a mutant or wildtype strains. Embryos were collected for two weeks or until completion of 5 breeding events. PFOS was maternally transferred to offspring independent of genotype throughout all breeding events in a dose-dependent manner, ranging from 2.77 to 23.72 ng/embryo in Nrf2a wildtype and 2.40 to 15.80 ng/embryo in Nrf2a mutants. Although embryo viability at collection was not impacted by maternal PFOS exposure, developmental effects related to nutrient uptake, growth and pancreatic ß-cell morphology were observed and differed based on genotype. Triglyceride levels were increased in Nrf2a wildtype eggs from the highest PFOS group. In Nrf2a wildtype larvae there was a decrease in yolk sac uptake while in Nrf2a mutants there was an increase. Additionally, there was a significant decrease in pancreatic ß-cell (islet) area in wildtype larvae from the 0.14 mg/L PFOS accompanied by an increase in the prevalence of abnormal islet morphologies compared to controls. Abnormal morphology was also observed in the 0.02 and 0.08 mg/L PFOS groups. Interestingly, in Nrf2a mutants there was a significant increase in the pancreatic ß-cell area in the 0.02 and 0.08 mg/L PFOS groups and no changes in the prevalence of abnormal islet morphologies. These results suggest that the regulation of processes like nutrient consumption, growth and pancreatic ß-cell development are at least partially modulated by the presence of a functional Nrf2a transcriptomic response. Overall, preconception exposure to environmental pollutants, such as PFOS, may impact the maturing oocyte and cause subtle changes that can ultimately impact offspring health and development.

HoloCamera: Advanced Volumetric Capture for Cinematic-Quality VR Applications.

High-precision virtual environments are increasingly important for various education, simulation, training, performance, and entertainment applications. We present HoloCamera, an innovative volumetric capture instrument to rapidly acquire, process, and create cinematic-quality virtual avatars and scenarios. The HoloCamera consists of a custom-designed free-standing structure with 300 high-resolution RGB cameras mounted with uniform spacing spanning the four sides and the ceiling of a room-sized studio. The light field acquired from these cameras is streamed through a distributed array of GPUs that interleave the processing and transmission of 4K resolution images. The distributed compute infrastructure that powers these RGB cameras consists of 50 Jetson AGX Xavier boards, with each processing unit dedicated to driving and processing imagery from six cameras. A high-speed Gigabit Ethernet network fabric seamlessly interconnects all computing boards. In this systems paper, we provide an in-depth description of the steps involved and lessons learned in constructing such a cutting-edge volumetric capture facility that can be generalized to other such facilities. We delve into the techniques employed to achieve precise frame synchronization and spatial calibration of cameras, careful determination of angled camera mounts, image processing from the camera sensors, and the need for a resilient and robust network infrastructure. To advance the field of volumetric capture, we are releasing a high-fidelity static light-field dataset, which will serve as a benchmark for further research and applications of cinematic-quality volumetric light fields.

Food preference-based screening method for identification of effectors of substance use disorders using Caenorhabditis elegans.

Substance use disorder (SUD) affects over 48 million Americans aged 12 and over. Thus, identifying novel chemicals contributing to SUD will be critical for developing efficient prevention and mitigation strategies. Considering the complexity of the actions and effects of these substances on human behavior, a high-throughput platform using a living organism is ideal. We developed a quick and easy screening assay using Caenorhabditis elegans. C. elegans prefers high-quality food (Escherichia coli HB101) over low-quality food (Bacillus megaterium), with a food preference index of approximately 0.2, defined as the difference in the number of worms at E. coli HB101 and B. megaterium over the total worm number. The food preference index was significantly increased by loperamide, a µ-opioid receptor (MOPR) agonist, and decreased by naloxone, a MOPR antagonist. These changes depended on npr-17, a C. elegans homolog of opioid receptors. In addition, the food preference index was significantly increased by arachidonyl-2'-chloroethylamide, a cannabinoid 1 receptor (CB1R) agonist, and decreased by rimonabant, a CB1R inverse agonist. These changes depended on npr-19, a homolog of CB1R. These results suggest that the conserved opioid and endocannabinoid systems modulate the food preference behaviors of C. elegans. Finally, the humanoid C. elegans strains where npr-17 was replaced with human MOPR and where npr-19 was replaced with human CB1R phenocopied the changes in food preference by the drug treatment. Together, the current results show that this method can be used to rapidly screen the potential effectors of MOPR and CB1R to yield results highly translatable to humans.

Comparing the effects of developmental exposure to alpha lipoic acid (ALA) and perfluorooctanesulfonic acid (PFOS) in zebrafish (Danio rerio).

Alpha lipoic acid (ALA) is a dietary supplement that has been used to treat a wide range of diseases, including obesity and diabetes, and have lipid-lowering effects, making it a potential candidate for mitigating dyslipidemia resulting from exposures to the per- and polyfluoroalkyl substance (PFAS) family member perfluorooctanesulfonic acid (PFOS). ALA can be considered a non-fluorinated structural analog to PFOS due to their similar 8-carbon chain and amphipathic structure, but, unlike PFOS, is rapidly metabolized. PFOS has been shown to reduce pancreatic islet area and induce ß-cell lipotoxicity, indicating that changes in ß-cell lipid microenvironment is a mechanism contributing to hypomorphic islets. Due to structural similarities, we hypothesized that ALA may compete with PFOS for binding to proteins and distribution throughout the body to mitigate the effects of PFOS exposure. However, ALA alone reduced islet area and fish length, with several morphological endpoints indicating additive toxicity in the co-exposures. Individually, ALA and PFOS increased fatty acid uptake from the yolk. ALA alone increased liver lipid accumulation, altered fatty acid profiling and modulated PPARÉ£ pathway signaling. Together, this work demonstrates that ALA and PFOS have similar effects on lipid uptake and metabolism during embryonic development in zebrafish.

Zirconium and hafnium catalyzed C-C single bond hydroboration.

Selective cleavage and subsequent functionalization of C-C single bonds present a fundamental challenge in synthetic organic chemistry. Traditionally, the activation of C-C single bonds has been achieved using stoichiometric transition-metal complexes. Recently, examples of catalytic processes were developed in which use is made of precious metals. However, the use of inexpensive and Earth-abundant group IV metals for catalytic C-C single-bond cleavage is largely underdeveloped. Herein, the zirconium-catalyzed C-C single-bond cleavage and subsequent hydroboration reactions is realized using Cp2ZrCl2 as a catalytic system. A series of structures of various γ-boronated amines are readily obtained, which are otherwise difficult to obtain. Mechanistic studies disclose the formation of a N-ZrIV species, and then a ß-carbon elimination route is responsible for C-C single bond activation. Besides zirconium, hafnium exhibits a similar performance for this transformation.

T4SEpp: A pipeline integrating protein language models to predict bacterial type IV secreted effectors.

Many pathogenic bacteria use type IV secretion systems (T4SSs) to deliver effectors (T4SEs) into the cytoplasm of eukaryotic cells, causing diseases. The identification of effectors is a crucial step in understanding the mechanisms of bacterial pathogenicity, but this remains a major challenge. In this study, we used the full-length embedding features generated by six pre-trained protein language models to train classifiers predicting T4SEs and compared their performance. We integrated three modules into a model called T4SEpp. The first module searched for full-length homologs of known T4SEs, signal sequences, and effector domains; the second module fine-tuned a machine learning model using data for a signal sequence feature; and the third module used the three best-performing pre-trained protein language models. T4SEpp outperformed other state-of-the-art (SOTA) software tools, achieving ∼0.98 accuracy at a high specificity of ∼0.99, based on the assessment of an independent validation dataset. T4SEpp predicted 13 T4SEs from Helicobacter pylori, including the well-known CagA and 12 other potential ones, among which eleven could potentially interact with human proteins. This suggests that these potential T4SEs may be associated with the pathogenicity of H. pylori. Overall, T4SEpp provides a better solution to assist in the identification of bacterial T4SEs and facilitates studies of bacterial pathogenicity. T4SEpp is freely accessible at https://bis.zju.edu.cn/T4SEpp.

HALD, a human aging and longevity knowledge graph for precision gerontology and geroscience analyses.

Human aging is a natural and inevitable biological process that leads to an increased risk of aging-related diseases. Developing anti-aging therapies for aging-related diseases requires a comprehensive understanding of the mechanisms and effects of aging and longevity from a multi-modal and multi-faceted perspective. However, most of the relevant knowledge is scattered in the biomedical literature, the volume of which reached 36 million in PubMed. Here, we presented HALD, a text mining-based human aging and longevity dataset of the biomedical knowledge graph from all published literature related to human aging and longevity in PubMed. HALD integrated multiple state-of-the-art natural language processing (NLP) techniques to improve the accuracy and coverage of the knowledge graph for precision gerontology and geroscience analyses. Up to September 2023, HALD had contained 12,227 entities in 10 types (gene, RNA, protein, carbohydrate, lipid, peptide, pharmaceutical preparations, toxin, mutation, and disease), 115,522 relations, 1,855 aging biomarkers, and 525 longevity biomarkers from 339,918 biomedical articles in PubMed. HALD is available at https://bis.zju.edu.cn/hald .

CropGF: a comprehensive visual platform for crop gene family mining and analysis.

A gene family refers to a group of genes that share a common ancestry and encode proteins or RNA molecules with similar functions or structural features. Gene families play a crucial role in determining the traits of plants and can be utilized to develop new crop varieties. Therefore, a comprehensive database of gene family is significant for gaining deep insight into crops. To address this need, we have developed CropGF (https://bis.zju.edu.cn/cropgf), a comprehensive visual platform that encompasses six important crops (rice, wheat, maize, barley, sorghum and foxtail millet) and one model plant (Arabidopsis), as well as genomics, transcriptomics and proteomics data for gene family mining and analysis, covering a total of 314 611 genes and 4399 types of domains. CropGF provides a versatile search system that allows for the identification of gene families and their members in a single crop or multiple crops. Users can customize their search based on gene family domains and/or homology using keywords or BLAST. To enhance usability, we have collected the corresponding ID information from various public databases for both genes and domains. Furthermore, CropGF comprises numerous downstream analysis modules, such as ka/ks analysis, phylogenetic tree construction, subcellular localization analysis and more. These visually-displayed modules provide intuitive insights into gene expression patterns, gene family expansion and functional relationships across different molecular levels and different species. We believe that CropGF will be a valuable resource for deep mining and analysis in future studies of crop gene families. Database URL https://bis.zju.edu.cn/cropgf.

The application of non-uniform magnetic field for thermal enhancement of the nanofluid flow inside the U-turn pipe at solar collectors.

The improvement of heat transfer inside the solar heat exchangers is important for the development of solar energy in an urban area. In this study, the usage of a non-uniform magnetic field on the thermal efficiency of the nanofluid (Fe3O4) streaming inside the U-turn pipe of solar heat exchangers is examined. Computational fluid dynamic is applied to visualize the nanofluid flow inside the solar heat exchanger. The role of magnetic intensity and Reynolds number on thermal efficiency are fully investigated. The effect of single and triple sources of the magnetic field is also studied in our research. Obtained results indicate that the usage of the magnetic field results in the production of vortex in the base fluid and heat transfer improves inside the domain. Our finding indicates that the usage of the magnetic field with Mn = 25 K would improve the average heat transfer by about 21% along the U-turn pipe of solar heat exchangers.

Basic helix-loop-helix transcription factor PxbHLH02 enhances drought tolerance in Populus (Populus simonii × P. nigra).

The basic helix-loop-helix (bHLH) transcription factors (TFs) are involved in plant morphogenesis and various abiotic and biotic stress responses. However, further exploration is required of drought-responsive bHLH family members and their detailed regulatory mechanisms in Populus. Two bHLH TF genes, PxbHLH01/02, were identified in Populus simonii × P. nigra and cloned. The aim of this study was to examine the role of bHLH TFs in drought tolerance in P. simonii × P. nigra. The results showed that the amino acid sequences of the two genes were homologous to Arabidopsis thaliana UPBEAT1 (AtUPB1) and overexpression of PxbHLH01/02 restored normal root length in the AtUPB1 insertional mutant (upb1-1). The PxbHLH01/02 gene promoter activity analysis suggested that they were involved in stress responses and hormone signaling. Furthermore, Arabidopsis transgenic lines overexpressing PxbHLH01/02 exhibited higher stress tolerance compared with the wild-type. Populus simonii × P. nigra overexpressing PxbHLH02 increased drought tolerance and exhibited higher superoxide dismutase and peroxidase activities, lower H2O2 and malondialdehyde content, and lower relative conductivity. The results of transcriptome sequencing (RNA-seq) and quantitative real-time PCR suggested that the response of PxbHLH02 to drought stress was related to abscisic acid (ABA) signal transduction. Overall, the findings of this study suggest that PxbHLH02 from P. simonii × P. nigra functions as a positive regulator of drought stress responses by regulating stomatal aperture and promoting ABA signal transduction.

Nrf2a dependent and independent effects of early life exposure to 3,3'-dichlorobiphenyl (PCB-11) in zebrafish (Danio rerio).

The environmental pollutant 3,3'-dichlorobiphenyl (PCB-11) is a lower-chlorinated polychlorinated biphenyl (PCB) congener present in air and water samples. Both PCB-11 and its metabolite, 4-PCB-11-Sulfate, are detected in humans, including in pregnant women. Previous research in zebrafish (Danio rerio) has shown that 0.2 µM exposures to 4-PCB-11-Sulfate starting at 1 day post fertilization (dpf) increase hepatic neutral lipid accumulation in larvae at 15 dpf. Here, we explored whether nuclear factor erythroid 2-related factor 2 (Nrf2), known as the master-regulator of the adaptive response to oxidative stress, contributes to metabolic impacts of 4-PCB-11-Sulfate. For this work, embryos were collected from homozygous wildtype or Nrf2a mutant adult zebrafish that also express GFP in pancreatic ß-cells, rendering Tg(ins:GFP;nrf2afh318+/+) and Tg(ins:GFP;nrf2afh318-/-) lines. Exposures were conducted from 1-15 dpf to either 0.05% DMSO or DMSO-matched 0.2 µM 4-PCB-11-Sulfate, and at 15 dpf subsets of larvae were imaged for overall morphology, primary pancreatic islet area, and collected for fatty acid profiling and RNAseq. At 15 dpf, independent of genotype, fish exposed to 4-PCB-11-Sulfate survived significantly more at 80-85% compared to 65-73% survival for unexposed fish, and had primary pancreatic islets 8% larger compared to unexposed fish. Fish growth at 15 dpf was dependent on genotype, with Nrf2a mutant fish a significant 3-5% shorter than wildtype fish, and an interaction effect was observed where Nrf2a mutant fish exposed to 4-PCB-11-Sulfate experienced a significant 29% decrease in the omega-3 fatty acid DHA compared to unexposed mutant fish. RNAseq revealed 308 differentially expressed genes, most of which were dependent on genotype. These findings suggest that Nrf2a plays an important role in growth as well as for DHA production in the presence of 4-PCB-11-Sulfate. Further research would be beneficial to understand the importance of Nrf2a throughout the lifecourse, especially in the context of toxicant exposures.

Estimating Biomass and Carbon Sequestration Capacity of Phragmites australis Using Remote Sensing and Growth Dynamics Modeling: A Case Study in Beijing Hanshiqiao Wetland Nature Reserve, China.

Estimating the biomass of Phragmites australis (Cav.) Trin. ex Steud., i.e., a common wetland macrophyte, and the associated carbon sequestration capacity has attracted increasing attention. Hanshiqiao Wetland Nature Reserve (HWNR) is a large P. australis wetland in Beijing, China, and provides an ideal case study site for such purpose in an urban setting. In this study, an existing P. australis growth dynamics model was adapted to estimate the plant biomass, which was in turn converted to the associated carbon sequestration capacity in the HWNR throughout a typical year. To account for local differences, the modeling parameters were calibrated against the above-ground biomass (AGB) of P. australis retrieved from hyperspectral images of the study site. We also analyzed the sensitivity of the modeling parameters and the influence of environmental factors, particularly the nutrient availability, on the growth dynamics and carbon sequestration capacity of P. australis. Our results show that the maximum AGB and below-ground biomass (BGB) of P. australis in the HWNR are 2.93 × 103 and 2.49 × 103 g m-2, respectively, which are higher than the reported level from nearby sites with similar latitudes, presumably due to the relatively high nutrient availability and more suitable inundation conditions in the HWNR. The annual carbon sequestration capacity of P. australis in the HWNR was estimated to be 2040.73 gC m-2 yr-1, which was also found to be highly dependent on nutrient availability, with a 50% increase (decrease) in the constant of the nutrient availability KNP, resulting in a 12% increase (23% decrease) in the annual carbon sequestration capacity. This implies that a comprehensive management of urban wetlands that often encounter eutrophication problems to synergize the effects of nutrient control and carbon sequestration is worth considering in future practices.

Visible-Light-Promoted Unsymmetrical Phosphine Synthesis from Benzylamines.

Herein, by applying visible-light photoredox catalysis, we have achieved the catalytic deaminative alkylation of diphenylphosphine and phenyl phosphine with benzylamine-derived Katritzky salts at room temperature. The use of Eosin Y as photoredox catalyst and visible light can largely promote the reaction. A series of unsymmetrical tertiary phosphines were successfully synthesized, including phosphines with three different substituents that are otherwise difficult to obtain.

Voltammetric and galvanostatic methods for measuring hydrogen crossover in fuel cell.

Hydrogen crossover rate is an important indicator for characterizing the membrane degradation and failure in proton exchange membrane fuel cell. Several electrochemical methods have been applied to quantify it. But most of established methods are too rough to support follow-up applications. In this paper, a systematic and consistent theoretical foundation for electrochemical measurements of hydrogen crossover is established for the first time. Different electrochemical processes occurring throughout the courses of applying potentiostatic or galvanostatic excitations on fuel cell are clarified, and the linear current-voltage behavior observed in the steady-state voltammogram is reinterpreted. On this basis, we propose a modified galvanostatic charging method with high practicality to achieve accurate electrochemical measurement of hydrogen crossover, and the validity of this method is fully verified. This research provides an explicit framework for implementation of galvanostatic charging method and offers deeper insights into the principles of electrochemical methods for measuring hydrogen crossover.

TI-ADC multi-channel mismatch estimation and calibration in ultra-high-speed optical signal acquisition system.

This article presents a method to calibrate a 16-channel 40 GS/s time-interleaved analog-to-digital converter (TI-ADC) based on channel equalization and Monte Carlo method. First, the channel mismatch is estimated by the Monte Carlo method, and equalize each channel to meet the calibration requirement. This method does not require additional hardware circuits, every channel can be compensated. The calibration structure is simple and the convergence speed is fast, besides, the ADC is worked in background mode, which does not affect the conversion. The prototype, implemented in 28 nm CMOS, reaches a 41 dB SFDR with an input signal of 1.2 GHz and 5 dBm after the proposed background offset and gain mismatch calibration. Compared with previous works, the spurious-free dynamic range (SFDR) and the effective number of bits (ENOB) are better, the estimation accuracy is higher, the error is smaller and the faster speed of convergence improves the efficiency of signal processing.

Caenorhabditis elegans as a model for obesity research.

Caenorhabditis elegans, a free-living nematode, is an animal model that has been extensively employed in a variety of research fields, including in the study of obesity. Its favorable features include its compact size, short life cycle, large brood size, easy handling, low cost, availability of complete genetic information, 65% conserved human diseases-associated genes, relatively easy genetic manipulation, and research using Caenorhabditis elegans does not require approvals by the Institutional Animal Care and Use Committee. These advantages make Caenorhabditis elegans a great in vivo model for life science research including obesity research. In this review, we provide graphic overviews of Caenorhabditis elegans' basic anatomy, growth conditions, routes of compound delivery, and fat metabolism, both synthesis and degradation pathways, including major signaling pathways involved. Our aim is to provide an overview for researchers interested in applying C. elegans as an in vivo model for the screening and identification of anti-obesity bioactive compounds prior to testing in vertebrate animal models.

Site-Fixed Hydroboration of Terminal and Internal Alkenes using BX3 /i Pr2 NEt*.

An unprecedented and general hydroboration of alkenes with BX3 (X=Br, Cl) as the boration reagent in the presence of i Pr2 NEt is reported. The addition of i Pr2 NEt not only suppresses alkene polymerization and haloboration side reactions but also provides an "H" source for hydroboration. More importantly, the site-fixed installation of a boryl group at the original position of the internal double bond is readily achieved in contrast to conventional transition-metal-catalyzed hydroboration processes. Further application to the synthesis of 1,n-diborylalkanes (n=3-10) is also demonstrated. Preliminary mechanistic studies reveal a major reaction pathway that involves radical species and operates through a frustrated Lewis pair type single-electron-transfer mechanism.

mPPI: a database extension to visualize structural interactome in a one-to-many manner.

Protein-protein interaction (PPI) databases with structural information are useful to investigate biological functions at both systematic and atomic levels. However, most existing PPI databases only curate binary interactome. From the perspective of the display and function of PPI, as well as the structural binding interface, the related database and resources are summarized. We developed a database extension, named mPPI, for PPI structural visualization. Comparing with the existing structural interactomes that curate resolved PPI conformation in pairs, mPPI can visualize target protein and its multiple interactors simultaneously, which facilitates multi-target drug discovery and structure prediction of protein macro-complexes. By employing a protein-protein docking algorithm, mPPI largely extends the coverage of structural interactome from experimentally resolved complexes. mPPI is designed to be a customizable and convenient plugin for PPI databases. It possesses wide potential applications for various PPI databases, and it has been used for a neurodegenerative disease-related PPI database as demonstration. Scripts and implementation guidelines of mPPI are documented at the database tool website. Database URL  http://bis.zju.edu.cn/mppi/.

Evolving tides aggravate nuisance flooding along the U.S. coastline.

Nuisance flooding (NF) is defined as minor, nondestructive flooding that causes substantial, accumulating socioeconomic impacts to coastal communities. While sea-level rise is the main driver for the observed increase in NF events in the United States, we show here that secular changes in tides also contribute. An analysis of 40 tidal gauge records from U.S. coasts finds that, at 18 locations, NF increased due to tidal amplification, while decreases in tidal range suppressed NF at 11 locations. Estuaries show the largest changes in NF attributable to tide changes, and these can often be traced to anthropogenic alterations. Limited long-term measurements from estuaries suggest that the effects of evolving tides are more widespread than the locations considered here. The total number of NF days caused by tidal changes has increased at an exponential rate since 1950, adding ~27% to the total number of NF events observed in 2019 across locations with tidal amplification.