The interaction between proteins is one of the most important features of protein functions. In general, the protein-protein interactions (PPIs) network of an organism is very complex, consisting of huge amount of PPIs. Functional modules can be identified from the complex protein interaction networks. It follows that the investigation of functional modules will generate a better understanding of cellular organization, processes and functions. However, it is a great challenge to apply modularity analysis to under-studied organism, even though this organism has already been sequenced, as there are few or none experimental validated PPI data for them. Therefore, by integrating several bioinformatics methods, we provide a solution for modularity analysis of any sequenced organism. By this way, new information may be found for the organism in different level, such as protein-protein interaction, pathways or cellular process. For the computation part, it takes one to two weeks. The main impact factors are computer power and size of the PPI network. It takes longer time for the manually analysis of biological meanings of the modules.
Chaohu is a large freshwater lake. It plays an essential part in agriculture, life, and part of the industry. This study analyzed the heavy metals contents of copper (Cu), zinc (Zn), cadmium (Cd), mercury (Hg), arsenic (As), chromium (Cr), nickel (Ni), and lead (Pb) in sediments of the Chaohu Lake using inductively coupled plasma mass spectrometry. The distribution of some potential hazardous trace element in Chaohu Lake in the order as Zn (44.04 mg kg−1)>Cu (28.62 mg kg−1)>Cr (27.39 mg kg−1)>Pb (16.71 mg kg−1)≈Ni (16.22 mg kg−1)>As (5.89 mg kg−1)>Cd (0.14 mg kg−1)>Hg (0.04 mg kg−1). The results indicated that the selected heavy metals in the lake were practically uncontaminated, and the levels of selected potential hazardous elements varied from different sampling sites. Correlation analysis indicated that the selected potential hazardous element pollutant has co-contamination also occurs in sediments. However, in the center of Chaohu Lake, the primary contributor to the ecological risk was Cd (41%) and Hg (40%). Based on the PERI, the total potential ecological risk of selected heavy metals in the sediments of Chaohu Lake was light-contaminated.
Abstract Ruminants are important for global food security but emit the greenhouse gas methane. Rumen microorganisms break down complex carbohydrates to produce volatile fatty acids and molecular hydrogen. This hydrogen is mainly converted into methane by archaea, but can also be used by hydrogenotrophic acetogenic and respiratory bacteria to produce useful metabolites. A better mechanistic understanding is needed on how dietary carbohydrates influence hydrogen metabolism and methanogenesis. We profiled the composition, metabolic pathways, and activities of rumen microbiota in 24 beef cattle adapted to either fiber-rich or starch-rich diets. The fiber-rich diet selected for fibrolytic bacteria and methanogens resulting in increased fiber utilization, while the starch-rich diet selected for amylolytic bacteria and lactate utilizers, allowing the maintenance of a healthy rumen and decreasing methane production (p < 0.05). Furthermore, the fiber-rich diet enriched for hydrogenotrophic methanogens and acetogens leading to increased electron-bifurcating [FeFe]-hydrogenases, methanogenic [NiFe]- and [Fe]-hydrogenases and acetyl-CoA synthase, with lower dissolved hydrogen (42%, p < 0.001). In contrast, the starch-rich diet enriched for respiratory hydrogenotrophs with greater hydrogen-producing group B [FeFe]-hydrogenases and respiratory group 1d [NiFe]-hydrogenases. Parallel in vitro experiments showed that the fiber-rich selected microbiome enhanced acetate and butyrate production while decreasing methane production (p < 0.05), suggesting that the enriched hydrogenotrophic acetogens converted some hydrogen that would otherwise be used by methanogenesis. These insights into hydrogen metabolism and methanogenesis improve understanding of energy harvesting strategies, healthy rumen maintenance, and methane mitigation in ruminants.
The role of lipid metabolic reprogramming in the development of various types of cancer has already been established. However, the exact biological function and significance of the elongation of very-long-chain fatty acids (ELOVLs) gene family, which can affect fatty acid metabolism, is still not well understood in lung adenocarcinoma (LUAD). The aim of our study is to explore whether there are genes related to the pathogenesis of LUAD in the ELOVLs family, and even to guide clinical medication and potential prognostic indicators. Gene expression profiling interactive analysis (GEPIA), human protein atlas (HPA), cBioPortal, Kaplan–Meier (KM) plotter, single-sample Gene Set Enrichment Analysis (ssGSEA) algorithm and SubMap algorithms were utilized to analyze the role of ELOVLs in the LUAD. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, cell counting kit-8 (CCK8), colony formation, wound healing, transwell migration assays and fatty acid metabolism detection were employed to confirm the significant role of ELOVL6 in vitro experiment. Our results revealed that mRNA expression levels of ELOVL2, ELOVL4 and ELOVL6 and protein expression levels of ELOVL5 and ELOVL6 were elevated in LUAD tissues compared to normal subjects. The low-expressing ELOVL6 group showed superior overall survival (OS) and disease-specific survival (DSS) versus the high-expressing group. Meanwhile, patients with low-ELOVL6 expression were more sensitive to the 4 representative chemotherapeutic agents. In vitro, we revealed that interfering with ELOVL6 could influence the viability, proliferation, migration capacity and fatty acid metabolism of LUAD cells (A549 and H1299). Our study indicated that ELOVL6 could be used as an indicator to evaluate the prognosis and therapeutic effect, and even potential therapeutic target for patients with LUAD.
Abstract Background: Huangqi Guizhi Wuwu Decoction (HGWD) is a common prescription for the treatment of cervical radiculopathy (CR). And the effectiveness and safety of HGWD for CR were assessed in this study. Methods: Seven databases were searched. Randomized controlled trials involving HGWD alone or HGWD combined with conventional treatment were enrolled. The authors in pairs independently assessed the risk of bias and extracted the data. Results: Eight studies involving 783 participants with CR were included. Meta-analysis revealed that the efficacy of HGWD for CR was significantly superior compared with control treatment (risk ratio = 1.12, 95% confidence interval [CI]:1.06–1.19, Z = 3.71; P = .0002). Compare with control group, there is an increase in visual analog scale (mean difference [MD] = 0.99; 95% CI: 0.83–1.14; Z = 12.57; P < .00001). There was also an improvement of neck disability index (MD = 9.2; 95% CI: 8.28–10.11; Z = 19.75; P < .00001). Adverse events were not mentioned in the 8 trials. Conclusion: HGWD alone or HGWD plus other treatment may be helpful to patients with CR. However, the methodological quality of the randomized controlled trials was generally low. Larger and better-designed randomized controlled trials are recommended.
Introduction The implementation of the 10-year fishing ban in the Yangtze River has provided a crucial opportunity for the recovery of rare and endangered diadromous species, such as Coilia nasus . Methods In this study, we utilized electronic length–frequency analysis (ELEFAN) and length-based Bayesian biomass estimation (LBB) method to fit the body length data of C. nasus from the Yangtze River Estuary and its adjacent sea areas before and after the fishing ban (2019-2023), and the resource changes of C. nasus population were evaluated. Additionally, combined the catch production monitoring data from 2020 to 2022, we comprehensively analyzed the impact of the Yangtze River fishing ban on the recovery of C. nasus resources. Results The results showed that: (1) The proportion of quantity, weight and occurrence frequency of C. nasus in catches showed a significant increasing trend year by year. (2) 4,994 C. nasus were caught from 2021–2023, with body lengths ranging from 13–410 mm. In 2023, the average body length and weight of C. nasus had increased by 39.93% and 133.89%, respectively, from those in 2021. (3) ELEFAN estimated that the growth parameters after fishing ban, including asymptotic length, growth coefficient, and the theoretical age at length zero, were determined to be 42.92 cm, 0.43 year -1 , and -0.31 year, respectively. The total mortality rate, fishing mortality rate, and exploitation rate were determined to be 1.47 year -1 , 0.79 year -1 , and 0.54, respectively. (4) LBB estimated that the relative fishing mortality of C. nasus before the fishing ban increased from 1.22 in 2019 to 2.65 in 2020, while the relative biomass decreased from 0.34 to 0.22. After the fishing ban, the relative fishing mortality decreased from 0.85 in 2021 to 0.06 in 2023, and the relative biomass increased from 0.26 in 2021 to 0.90 in 2023, with a significant increase in 2022, indicating a clear recovery trend in C. nasus resources. Discussion By quantifying the resource characteristics of C. nasus before and after the 10-year fishing ban on the Yangtze River, this research revealed the impact of the ban and provided a reference for future systematic evaluations of the C. nasus population.
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