As a circadian organ, liver executes diverse functions in different phase of the circadian clock. This process is believed to be driven by a transcription program. Here, we present a transcription ...factor (TF) DNA-binding activity-centered multi-dimensional proteomics landscape of the mouse liver, which includes DNA-binding profiles of different TFs, phosphorylation, and ubiquitylation patterns, the nuclear sub-proteome, the whole proteome as well as the transcriptome, to portray the hierarchical circadian clock network of this tissue. The TF DNA-binding activity indicates diurnal oscillation in four major pathways, namely the immune response, glucose metabolism, fatty acid metabolism, and the cell cycle. We also isolate the mouse liver Kupffer cells and measure their proteomes during the circadian cycle to reveal a cell-type resolved circadian clock. These comprehensive data sets provide a rich data resource for the understanding of mouse hepatic physiology around the circadian clock.
The diffuse-type gastric cancer (DGC) is a subtype of gastric cancer with the worst prognosis and few treatment options. Here we present a dataset from 84 DGC patients, composed of a proteome of ...11,340 gene products and mutation information of 274 cancer driver genes covering paired tumor and nearby tissue. DGC can be classified into three subtypes (PX1-3) based on the altered proteome alone. PX1 and PX2 exhibit dysregulation in the cell cycle and PX2 features an additional EMT process; PX3 is enriched in immune response proteins, has the worst survival, and is insensitive to chemotherapy. Data analysis revealed four major vulnerabilities in DGC that may be targeted for treatment, and allowed the nomination of potential immunotherapy targets for DGC patients, particularly for those in PX3. This dataset provides a rich resource for information and knowledge mining toward altered signaling pathways in DGC and demonstrates the benefit of proteomic analysis in cancer molecular subtyping.
Transcription factors (TFs) drive various biological processes ranging from embryonic development to carcinogenesis. Here, we employ a recently developed concatenated tandem array of consensus TF ...response elements (catTFRE) approach to profile the activated TFs in 24 adult and 8 fetal mouse tissues on proteome scale. A total of 941 TFs are quantitatively identified, representing over 60% of the TFs in the mouse genome. Using an integrated omics approach, we present a TF network in the major organs of the mouse, allowing data mining and generating knowledge to elucidate the roles of TFs in various biological processes, including tissue type maintenance and determining the general features of a physiological system. This study provides a landscape of TFs in mouse tissues that can be used to elucidate transcriptional regulatory specificity and programming and as a baseline that may facilitate understanding diseases that are regulated by TFs.
Objective:
To investigate the application of modified elastic intramedullary nail and the outcomes between modified elastic stable intramedullary nailing and traditional elastic stable intramedullary ...nailing in children with distal tibial metaphyseal junction fracture.
Methods:
A retrospective study was conducted. From January 2018 to January 2021, a total of 36 children with distal tibial metaphyseal junction fracture were treated in our hospital. All of them were treated with closed reduction and elastic stable intramedullary nailing internal fixation. A total of 18 children were treated by modified elastic stable intramedullary nailing and 18 children were treated by traditional elastic stable intramedullary nailing. Postoperative imaging, clinical efficacy, and complications were analyzed.
Results:
The mean follow-up time was 20 (15–36) months in modified group and 22 (16–33) months in traditional group. There were no complications such as infection, loss of reduction, and unequal length of lower limbs in modified group while loss of reduction occurred in two cases in traditional group. In these two cases of loss of reduction, we preformed manual reduction and replacement of long leg casts, and there was no loss of reduction, and the patient achieved a good prognosis. In the last follow-up, American Orthopaedic Foot & Ankle Society score was used. In modified group, excellent outcome achieved in 17 cases, good outcome achieved in 1 case, and satisfactory therapeutic effect was achieved. In traditional elastic stable intramedullary nailing group, excellent outcome achieved in 14 cases, and good outcome achieved in 4 cases. There was no statistical difference in the scores between the two groups.
Conclusion:
It was concluded that modified elastic stable intramedullary nailing fixation is a safe and effective treatment.
The present study aimed to investigate the changes in volatile components and metabolites of Dendrobium officinale (D. officinale) juice fermented with starter cultures containing Saccharomycopsis ...fibuligera and Lactobacillus paracasei at 28 ℃ for 15 days and post-ripened at 4 ℃ for 30 days using untargeted metabolomics of liquid chromatography-mass spectrometry (LC-MS) and headspace solid-phase microextraction-gas chromatography (HS-SPME-GC-MS) before and after fermentation.
The results showed that the alcohol contents in the S. fibuligera group before fermentation and after fermentation were 444.806 ± 10.310 μg/mL and 510.999 ± 38.431 μg/mL, respectively. Furthermore, the alcohol content in the fermentation broth group inoculated with the co-culture of L. paracasei + S. fibuligera was 504.758 ± 77.914 μg/mL, containing a significant amount of 3-Methyl-1-butanol, Linalool, Phenylethyl alcohol, and 2-Methyl-1-propanol. Moreover, the Ethyl L (-)-lactate content was higher in the co-culture of L. paracasei + S. fibuligera group (7.718 ± 6.668 μg/mL) than in the L. paracasei (2.798 ± 0.443 μg/mL) and S. fibuligera monoculture groups (0 μg/mL). The co-culture of L. paracasei + S. fibuligera significantly promoted the metabolic production of ethyl L (-)-lactate in D. officinale juice. The differential metabolites screened after fermentation mainly included alcohols, organic acids, amino acids, nucleic acids, and their derivatives. Twenty-three metabolites, including 11 types of acids, were significantly up-regulated in the ten key metabolic pathways of the co-culture group. Furthermore, the metabolic pathways, such as pentose and glucuronate interconversions, the biosynthesis of alkaloids derived from terpenoid and polyketide, and aminobenzoate degradation were significantly up-regulated in the co-culture group. These three metabolic pathways facilitate the synthesis of bioactive substances, such as terpenoids, polyketides, and phenols, and enrich the flavor composition of D. officinale juice.
These results demonstrate that the co-culture of L. paracasei + S. fibuligera can promote the flavor harmonization of fermented products. Therefore, this study provides a theoretical basis for analyzing the flavor of D. officinale juice and the functional investigation of fermentation metabolites.
Eukaryotic cells store neutral lipids in cytoplasmic lipid droplets (LDs) enclosed in a monolayer of phospholipids and associated proteins LD proteins (LDPs). Growing evidence has demonstrated that ...LDPs play important roles in the pathogenesis of liver diseases. However, the composition of liver LDPs and the role of their alterations in hepatosteatosis are not well-understood. In this study, we performed liver proteome and LD sub-proteome profiling to identify enriched proteins in LDs as LDPs, and quantified their changes in a high-fat diet (HFD)-induced fatty liver model. Among 5,000 quantified liver proteins, 101 were enriched by greater than 10-fold in the LD sub-proteome and were classified as LDPs. Differential profiling of LDPs in HFD-induced fatty liver provided a list of candidate LDPs for functional investigation. We tested the function of an upregulated LDP, S100a10, in vivo with adenovirus-mediated gene silencing and found, unexpectedly, that knockdown of S100a10 accelerated progression of HFD-induced liver steatosis. The S100A10 interactome revealed a connection between S100A10 and lipid transporting proteins, suggesting that S100A10 regulates the development and formation of LDs by transporting and trafficking. This study identified LD-enriched sub-proteome in homeostatic as well as HFD-induced fatty livers, providing a rich resource for the LDP research field.
Construction projects are often executed in complex environments, and various uncertain factors (e.g., bad weather, machine breakdown) prolong activity duration in practice, which may cause project ...completion delays or profit reduction. Moreover, previous studies often optimized net present value or robustness in project scheduling separately, they neglected the linkage between the value of obtaining NPV and the capacity of tackling uncertainties in a project schedule. To achieve optimal profit and enhance the stability of a project schedule simultaneously, this study proposes a bi-objective optimization for resource-constrained robust construction project scheduling problem (RCRCPSP), which aims at optimizing NPV and robustness, and builds a bi-objective optimization model for the RCRCPSP based on five typical cash flow models. Then an ε-constraints procedure embedded with a genetic algorithm is proposed to solve the model. The ε-constraints procedure performs better than the multi-objective genetic algorithm proposed by the previous study through case study. Furthermore, the findings demonstrate that a trade-off relationship exists between NPV and robustness, and cash flow models have little impact on robustness, while the relaxed deadline can improve a project schedule with high robustness. The fruits of this study can help contractors balance the NPV and the robustness in an indeterministic environment.
Farmland conversion to forest is considered to be one of the effective measures to mitigate climate change. However, the impact of farmland conversion to forest land or grassland on soil CO2 emission ...in arid areas is unclear due to the lack of comparative information on soil organic carbon (SOC) mineralization of different conversion types. The SOC mineralization in 0-100 cm soil layer in farmland (FL), abandoned land (AL) and different ages (including 8, 15, 20 and 28 years) of Zanthoxylum bungeanum plantations were measured by laboratory incubation. The size and decomposition rate of fast pool (Cf) and slow pool (Cs) in different land-use types and soil layers were estimated by double exponential model. The results showed that: 1) Farmland conversion increased the cumulative CO2-C release (Cmin) and SOC mineralization efficiency, and those indexes in AL were higher than that in Z. bungeanum plantations. The Cmin and SOC mineralization efficiency of 0-100 cm soil increased with the ages of Z. bungeanum plantation. Both Cmin and SOC mineralization efficiency decreased with the increase of soil depth; 2) Both soil Cf and Cs increased after farmland converted to Z. bungeanum plantations and AL. The Cs in the same soil layer increased with the ages of Z. bungeanum plantation, and the Cf showed a "V" type with the increased ages of Z. bungeanum plantation. The Cf and Cs decreased with the increase of soil depth in all land-use types; 3) Farmland conversion increased the decomposition rate of Cf (k1) in all soil layer by 0.008-0.143 d-1 and 0.082-0.148 d-1 in Z. bungeanum plantations and AL, respectively. The k1 was obviously higher in the 0-20 cm soil layer than that in other soil layers, while the decomposition rate of Cs (k2) was not affected by FL conversion and soil depth; and 4) The initial soil chemical properties and enzyme activity affected SOC mineralization, especially the concentrations of total organic nitrogen (TON), SOC, easily oxidizable organic carbon (EOC) and microbial biomass carbon (MBC). It indicated that the conversion of farmland to Z. bungeanum plantations and AL increases SOC mineralization, especially in deeper soils, and it increased with the ages. The conversion of farmland to Z. bungeanum plantation is the optimal measure when the potential C sequestration of plant-soil system were taken in consideration.
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