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"Feng, Song"
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Physical Mechanisms of Summer Precipitation Variations in the Tarim Basin in Northwestern China
The Tarim basin (TB) in northwestern China is one of the most arid regions in the middle latitudes, where water is scarce year-round. This study investigates the variations of summer precipitation in the TB and their association with water vapor fluxes and atmospheric circulation. The results suggest that the variations of summer precipitation in the TB are dominated by the water vapor fluxes from the south and east, although the long-term mean water vapor mostly comes from the west. The anomalous water vapor fluxes are closely associated with the meridional teleconnection pattern around 50°–80°E and the zonal teleconnection pattern along the Asian westerly jet in summer. The meridional teleconnection connects central Asia and the tropical Indian Ocean; the zonal teleconnection resembles the “Silk Road pattern.” The two teleconnections lead to negative height anomalies in central Asia and positive height anomalies in the Arabian Sea and India and in northern central China. The anomalous pressure gradient force, caused by these height anomalies, leads to anomalous ascending motion in the TB and brings low-level moisture along the eastern periphery of the Tibetan Plateau and water vapor from the Arabian Sea passing over the Tibetan Plateau to influence precipitation development in the study region.
Journal Article
High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip
Global quantification of protein abundances in single cells could provide direct information on cellular phenotypes and complement transcriptomics measurements. However, single-cell proteomics is still immature and confronts many technical challenges. Herein we describe a nested nanoPOTS (N2) chip to improve protein recovery, operation robustness, and processing throughput for isobaric-labeling-based scProteomics workflow. The N2 chip reduces reaction volume to <30 nL and increases capacity to >240 single cells on a single microchip. The tandem mass tag (TMT) pooling step is simplified by adding a microliter droplet on the nested nanowells to combine labeled single-cell samples. In the analysis of ~100 individual cells from three different cell lines, we demonstrate that the N2 chip-based scProteomics platform can robustly quantify ~1500 proteins and reveal membrane protein markers. Our analyses also reveal low protein abundance variations, suggesting the single-cell proteome profiles are highly stable for the cells cultured under identical conditions.
Single-cell proteomics is an emerging technology but protein coverage, throughput and quantitation accuracy are often still insufficient. Here, the authors develop a nested nanowell chip that improves protein recovery, throughput and robustness of isobaric labeling-based quantitative single-cell proteomics.
Journal Article
Why Do Different Drought Indices Show Distinct Future Drought Risk Outcomes in the U.S. Great Plains?
Vigorous discussions and disagreements about the future changes in drought intensity in the U.S. Great Plains have been taking place recently within the literature. These discussions have involved widely varying estimates based on drought indices and model-based projections of the future. To investigate and understand the causes for such a disparity between these previous estimates, the authors analyzed the soil moisture at the near-surface soil layer and the entire soil column, as well as the Palmer drought severity index, the Palmer Z index, and the standardized precipitation and evaporation index using the output from the Community Climate System Model, version 4 (CCSM4), and 25 state-of-the-art climate models. These drought indices were computed using potential evapotranspiration estimated by the physically based Penman–Monteith method (PE_pm) and the empirically based Thornthwaite method (PE_th). The results showed that the short-term drought indices are similar to modeled surface soil moisture and show a small but consistent drying trend in the future. The long-term drought indices and the total column soil moisture, however, are consistent in projecting more intense future drought. When normalized, the drought indices with PE_th all show unprecedented future drying, while the drought indices with PE_pm show comparable dryness with the modeled soil moisture. Additionally, the drought indices with PE_pm are closely related to soil moisture during both the twentieth and twenty-first centuries. Overall, the drought indices with PE_pm, as well as the modeled total column soil moisture, suggest a widespread and very significant drying in the Great Plains toward the end of the century. The results suggest that the sharp contrasts about future drought risk in the Great Plains discussed in previous studies are caused by 1) comparing the projected changes in short-term droughts with that of the longterm droughts and/or 2) computing the atmospheric evaporative demand using an empirically based method (e.g., PE_th). The analysis here may be applied for drought projections in other regions across the globe.
Journal Article
Dysregulation of NCAPG, KNL1, miR-148a-3p, miR-193b-3p, and miR-1179 may contribute to the progression of gastric cancer
Background
Emerging evidence indicate that miRNAs play an important role on gastric cancer (GC) progression via regulating several downstream targets, but it is still partially uncovered. This study aimed to explore the molecular mechanisms of GC by comprehensive analysis of mRNAs and miRNA expression profiles.
Methods
The mRNA and miRNA expression profiles of GSE79973 and GSE67354 downloaded from Gene Expression Omnibus were used to analyze the differentially expressed genes (DEGs) and DE-miRNAs among GC tissues and normal tissues. Then, targets genes of DE-miRNAs were predicted and the DE-miRNA–DEG regulatory network was constructed. Next, function enrichment analysis of the overlapped genes between the predicted DE-miRNAs targets and DEGs was performed and a protein–protein interactions network of overlapped genes was constructed. Finally, RT-PCR analysis was performed to detect the expression levels of several key DEGs and DE-miRNAs.
Results
A set of 703 upregulated and 600 downregulated DEGs, as well as 8 upregulated DE-miRNAs and 27 downregulated DE-miRNAs were identified in GC tissue. hsa-miR-193b-3p and hsa-miR-148a-3p, which targeted most DEGs, were highlighted in the DE-miRNA–DEG regulatory network, as well as hsa-miR-1179, which targeted
KNL1
, was newly predicted to be associated with GC. In addition,
NCAPG
, which is targeted by miR-193b-3p, and
KNL1
, which is targeted by hsa-miR-1179, had higher degrees in the PPI network. RT-qPCR results showed that hsa-miR-148a-3p, hsa-miR-193b-3p, and hsa-miR-1179 were downregulated, and
NCAPG
and
KNL1
were upregulated in GC tissues; this is consistent with our bioinformatics-predicted results.
Conclusions
The downregulation of miR-193b-3p might contribute to GC cell proliferation by mediating the upregulation of
NCAPG
; as additionally, the downregulation of miR-193b-3p might contribute to the mitotic nuclear division of GC cells by mediating the upregulation of
KNL1
.
Journal Article
Purification and Characterization of Plantaricin ZJ5, a New Bacteriocin Produced by Lactobacillus plantarum ZJ5
The aim of this study is to investigate the antimicrobial potential of Lactobacillus plantarum ZJ5, a strain isolated from fermented mustard with a broad range of inhibitory activity against both Gram-positive and Gram-negative bacteria. Here we present the peptide plantaricin ZJ5 (PZJ5), which is an extreme pH and heat-stable. However, it can be digested by pepsin and proteinase K. This peptide has strong activity against Staphylococcus aureus. PZJ5 has been purified using a multi-step process, including ammonium sulfate precipitation, cation-exchange chromatography, hydrophobic interactions and reverse-phase chromatography. The molecular mass of the peptide was found to be 2572.9 Da using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The primary structure of this peptide was determined using amino acid sequencing and DNA sequencing, and these analyses revealed that the DNA sequence translated as a 44-residue precursor containing a 22-amino-acid N-terminal extension that was of the double-glycine type. The bacteriocin sequence exhibited no homology with known bacteriocins when compared with those available in the database, indicating that it was a new class IId bacteriocin. PZJ5 from a food-borne strain may be useful as a promising probiotic candidate.
Journal Article
Real-Time Detection of Unauthorized Unmanned Aerial Vehicles Using SEB-YOLOv8s
Aiming at real-time detection of UAVs, small UAV targets are easily missed and difficult to detect in complex backgrounds. To maintain high detection performance while reducing memory and computational costs, this paper proposes the SEB-YOLOv8s detection method. Firstly, the YOLOv8 network structure is reconstructed using SPD-Conv to reduce the computational burden and accelerate the processing speed while retaining more shallow features of small targets. Secondly, we design the AttC2f module and replace the C2f module in the backbone of YOLOv8s with it, enhancing the model’s ability to obtain accurate information and enriching the extracted relevant information. Finally, Bi-Level Routing Attention is introduced to optimize the Neck part of the network, reducing the model’s attention to interfering information and filtering it out. The experimental results show that the mAP50 of the proposed method reaches 90.5% and the accuracy reaches 95.9%, which are improvements of 2.2% and 1.9%, respectively, compared with the original model. The mAP50-95 is improved by 2.7%, and the model’s occupied memory size only increases by 2.5 MB, effectively achieving high-accuracy real-time detection with low memory consumption.
Journal Article
A Review of the Extraction and Determination Methods of Thirteen Essential Vitamins to the Human Body: An Update from 2010
Vitamins are a class of essential nutrients in the body; thus, they play important roles in human health. The chemicals are involved in many physiological functions and both their lack and excess can put health at risk. Therefore, the establishment of methods for monitoring vitamin concentrations in different matrices is necessary. In this review, an updated overview of the main pretreatments and determination methods that have been used since 2010 is given. Ultrasonic assisted extraction, liquid–liquid extraction, solid phase extraction and dispersive liquid–liquid microextraction are the most common pretreatment methods, while the determination methods involve chromatography methods, electrophoretic methods, microbiological assays, immunoassays, biosensors and several other methods. Different pretreatments and determination methods are discussed.
Journal Article
Jasmonic Acid Impairs Arabidopsis Seedling Salt Stress Tolerance Through MYC2-Mediated Repression of CAT2 Expression
High salinity causes ionic, osmotic, and oxidative stresses to plants, and the antioxidant enzyme Catalase2 (CAT2) plays a vital role in this process, while how
CAT2
expression is regulated during plant response to high salinity remains elusive. Here, we report that phytohormone jasmonic acid (JA) impairs plant salt stress tolerance by repressing
CAT2
expression in an MYC2-dependent manner. Exogenous JA application decreased plant salt stress tolerance while the
jar1
mutant with reduced bioactive JA-Ile accumulation showed enhanced salt stress tolerance. JA enhanced salt-induced hydrogen peroxide (H
2
O
2
) accumulation, while treatment with H
2
O
2
-scavenger glutathione compromised such effects of JA on plant H
2
O
2
accumulation and salt stress tolerance. In addition, JA repressed
CAT2
expression in salt-stressed wild-type plant but not in
myc2
, a mutant of the master transcriptional factor MYC2 in JA signaling, therefore, the
myc2
mutant exhibited increased salt stress tolerance. Further study showed that mutation of
CAT2
largely reverted lower reactive oxygen species (ROS) accumulation, higher CAT activity, and enhanced salt stress tolerance of the
myc2
mutant in
myc2 cat2-1
double mutant, revealing that
CAT2
functions downstream JA-MYC2 module in plant response to high salinity. Together, our study reveals that JA impairs Arabidopsis seedling salt stress tolerance through MYC2-mediated repression of
CAT2
expression.
Journal Article
High ORC6 expression is a prognostic indicator of poor survival in glioma patients
Precision therapy for glioma remains a major challenge due to tumor heterogeneity. The Origin Recognition Complex Subunit 6 (ORC6) is a crucial regulator of DNA replication initiation. This study aims to investigate the expression of ORC6 in gliomas and its relationship with survival rates and malignancy, while screening potential drugs targeting its functional network. By integrating multiple bioinformatics approaches with structure-based virtual screening, retrospective RNA sequencing data analysis was performed using patients from the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) databases. A protein-protein interaction (PPI) network was constructed from ORC6-coexpressed genes to identify core hubs. Molecular docking was employed to screen a library of natural compounds and known drugs against these hub targets. Research has revealed that ORC6 is significantly upregulated in high-grade gliomas, with its elevated expression associated with poor survival outcomes and immune inflammatory responses. Network analysis identified five core hub genes (ORC1, ORC2, MCM2, MCM6, CDC45) central to DNA replication. Molecular docking revealed that several compounds, including the natural flavonoid Baicalein and the FDA-approved drug Palbociclib, exhibited high binding affinity to these hub targets. ORC6 represents a highly promising novel target for precision therapy in glioma. Potential approaches to target this pathway include disrupting the ORC6-replication axis using existing drugs (such as palbociclib) or natural products (such as baicalin).
Journal Article