Displaying publications 61 - 80 of 158 in total

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  1. Solid encapsulation of lauric acid into "empty" V-type starch: Structural characteristics and emulsifying properties
    Huang L, Li S, Tan CP, Feng Y, Zhang B, Fu X, et al.
    Carbohydr Polym, 2021 Sep 01;267:118181.
    PMID: 34119149 DOI: 10.1016/j.carbpol.2021.118181
    Lauric acid was introduced into "Empty" V-type starch using a solid encapsulation method. The structural characteristics and emulsifying properties of the starch-fatty acid complex (SFAC) were explored as a function of the complexing temperature. X-ray diffraction and differential scanning calorimetry confirmed that SFAC was mainly composed of type-I amylose inclusion complexes. Contact angle measurements revealed that the hydrophobic properties of SFAC were closely related to the temperature-regulated complex index. The particle size range of SFAC gradually increased as the complexing temperature increased. The SFAC-stabilized Pickering emulsion at c of 5% and Φ of 40-60% possessed a small droplet size and long-term storage stability for up to 30 days, resulting from the formation of a gel-like network. This study provides new insight into the design of hydrophobic modified starch as a novel and multifunctional emulsifier and is of great help in the development of starch-based Pickering emulsion gels.
  2. Fulltext Characterization and Kinetic Studies of Poly(vinylidene fluoride-co-hexafluoropropylene) Polymer Inclusion Membrane for the Malachite Green Extraction
    Soo JAL, Makhtar MMZ, Shoparwe NF, Otitoju TA, Mohamad M, Tan LS, et al.
    Membranes (Basel), 2021 Aug 31;11(9).
    PMID: 34564493 DOI: 10.3390/membranes11090676
    Textile industry effluent contains a high amount of toxic colorants. These dyes are carcinogenic and threats to the environment and living beings. In this study, poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-co-HFP) was used as the based polymer for PIMs with bis-(2-ethylhexyl) phosphate (B2EHP) and dioctyl phthalate (DOP) as the carrier and plasticizer. The fabricated PIMs were employed to extract the cation dye (Malachite Green; MG) from the feeding phase. PIMs were also characterized by scanning electron microscopy (SEM), atomic force microscope (AFM), contact angle, water uptake, Fourier-transform infrared spectroscopy (FTIR) and ions exchange capacity. The performance of the PIMs was investigated under various conditions such as percentage of carrier and initial dye concentration. With permeability and flux values of 0.1188 cm/min and 1.1913 mg cm/min, PIM produced with 18% w/w PVDF-co-HFP, 21% w/w B2EHP, 1% w/w DOP and 40% w/w THF and was able to achieve more than 97% of MG extraction. The experimental data were then fitted with a pseudo-second-order (PSO) model, and the calculated R2 value was ~0.99. This shows that the data has a good fit with the PSO model. PIM is a potential alternative technology in textile industry effluent treatment; however, the right formulation is crucial for developing a highly efficient membrane.
  3. Deletion of Plasma Membrane Malate Transporters Increased Lipid Accumulation in the Oleaginous Fungus Mucor circinelloides WJ11
    Yang J, Cánovas-Márquez JT, Li P, Li S, Niu J, Wang X, et al.
    J Agric Food Chem, 2021 Aug 25;69(33):9632-9641.
    PMID: 34428900 DOI: 10.1021/acs.jafc.1c03307
    Malate as an important intermediate metabolite, its subcellular location, and concentration have a significant impact on fungal lipid metabolism. Previous studies showed that the mitochondrial malate transporter plays an important role in lipid accumulation in Mucor circinelloides by manipulating intracellular malate concentration. However, the role of plasma membrane malate transporters in oleaginous fungi remains unexplored. Therefore, in this work, two plasma membrane malate transporters "2-oxoglutarate:malate antiporters" (named SoDIT-a and SoDIT-b) of M. circinelloides WJ11 were deleted, and the consequences in growth capacity, lipid accumulation, and metabolism were analyzed. The results showed that deletion of sodit-a or/and sodit-b reduced the extracellular malate, confirming that the products of both genes participate in malate transportation. In parallel, the lipid contents in mutants increased approximately 10-40% higher than that in the control strain, suggesting that the defect in plasma membrane malate transport results in an increase of malate available for lipid biosynthesis. Furthermore, transcriptional analysis showed that the expression levels of multiple key genes involved in the lipid biosynthesis were also increased in the knockout mutants. To the best of our knowledge, this is the first report that demonstrated the association between plasma membrane malate transporters and lipid accumulation in M. circinelloides.
  4. Fulltext Effects of resistance training on gait velocity and knee adduction moment in knee osteoarthritis patients: a systematic review and meta-analysis
    Li S, Ng WH, Abujaber S, Shaharudin S
    Sci Rep, 2021 08 09;11(1):16104.
    PMID: 34373507 DOI: 10.1038/s41598-021-95426-4
    The systematic review aimed to analyze the effects of resistance training in knee osteoarthritis (OA) rehabilitation from a biomechanical perspective. A meta-analysis was performed to determine the potential benefits of resistance training on patients with knee OA. Relevant studies based on the inclusion and exclusion criteria were selected from CENTRAL, PubMed, Scopus, and Web of Science databases inception to August 2020. Outcome measures included gait velocity and knee adduction moment (KAM). The mean differences of the data with a 95% confidence interval were analyzed using STATA 15.1 software The search identified eight studies that satisfied all the inclusion criteria, in which 164 patients were involved in gait velocity studies and another 122 patients were part of KAM studies. Analysis of the pooled data showed that resistance training significantly improved the gait velocity in patients with knee OA (p s. However, resistance training had no significant effect on improving KAM in patients with knee OA (p = 0.98, z = 0.03), ES (95% CI) = 0.00 (- 0.16, 0.16) percentage of body weight × height (%BW × Ht). Therefore, resistance training may enhance gait velocity but not KAM in knee OA patients. The protocol was registered at PROSPERO (registration number: CRD42020204897).
  5. Fermentation of blueberry juices using autochthonous lactic acid bacteria isolated from fruit environment: Fermentation characteristics and evolution of phenolic profiles
    Li S, Tao Y, Li D, Wen G, Zhou J, Manickam S, et al.
    Chemosphere, 2021 Aug;276:130090.
    PMID: 33740651 DOI: 10.1016/j.chemosphere.2021.130090
    In this study, 4 Lactobacillus plantarum strains and 5 Lactobacillus fermentum strains adapting well to the unfavorable fruit system were isolated under different fruit environments. The fermentation ability of these autochthonous lactic acid bacteria (LAB) strains in blueberry juice, and the influence of microbial metabolism on juice composition were explored. After 48 h of fermentation, the viable cell counts exceeded 10.0 log CFU/mL, malic acid content decreased from 511.47 ± 10.50 mg/L to below 146.38 ± 3.79 mg/L, and lactic acid content increased from 0 mg/L to above 2184.90 ± 335.80 mg/L. Moreover, the metabolism of these strains exerted a profound influence on the phenolic composition of juice. Total phenolic content in blueberry juice increased by 6.1-81.2% under lactic acid fermentation, and the antioxidant capacity in vitro enhanced by at least 34.0%. Anthocyanin content showed a declining trend, while the profile of non-anthocyaninic phenolics exhibited complex changes. The increments of rutin, myricetin and gallic acid contents through 48 h lactic acid fermentation exceeded 136%, 71% and 38%, respectively. Instead, the contents of p-hydroxybenzoic acid and caffeic acid decreased with fermentation. Overall, Lactobacillus plantarum LSJ-TY-HYB-T9 and LSJ-TY-HYB-T7, and Lactobacillus fermentum LSJ-TY-HYB-C22 and LSJ-TY-HYB-L16 could be the suitable strains to produce fermented fruit juices, including blueberry in practical applications.
  6. Fulltext Exosomal miR-224 contributes to hemolymph microbiota homeostasis during bacterial infection in crustacean
    Gong Y, Wei X, Sun W, Ren X, Chen J, Aweya JJ, et al.
    PLoS Pathog, 2021 08;17(8):e1009837.
    PMID: 34379706 DOI: 10.1371/journal.ppat.1009837
    It is well known that exosomes could serve as anti-microbial immune factors in animals. However, despite growing evidences have shown that the homeostasis of the hemolymph microbiota was vital for immune regulation in crustaceans, the relationship between exosomes and hemolymph microbiota homeostasis during pathogenic bacteria infection has not been addressed. Here, we reported that exosomes released from Vibrio parahaemolyticus-infected mud crabs (Scylla paramamosain) could help to maintain the homeostasis of hemolymph microbiota and have a protective effect on the mortality of the host during the infection process. We further confirmed that miR-224 was densely packaged in these exosomes, resulting in the suppression of HSP70 and disruption of the HSP70-TRAF6 complex, then the released TRAF6 further interacted with Ecsit to regulate the production of mitochondrial ROS (mROS) and the expression of Anti-lipopolysaccharide factors (ALFs) in recipient hemocytes, which eventually affected hemolymph microbiota homeostasis in response to the pathogenic bacteria infection in mud crab. To the best of our knowledge, this is the first document that reports the role of exosome in the hemolymph microbiota homeostasis modulation during pathogen infection, which reveals the crosstalk between exosomal miRNAs and innate immune response in crustaceans.
  7. Fulltext Author Correction: Novel Hybrid Evolutionary Algorithms for Spatial Prediction of Floods
    Bui DT, Panahi M, Shahabi H, Singh VP, Shirzadi A, Chapi K, et al.
    Sci Rep, 2021 Jul 20;11(1):15152.
    PMID: 34285263 DOI: 10.1038/s41598-021-93957-4
  8. Fulltext Predicting the environmental suitability for onchocerciasis in Africa as an aid to elimination planning
    Cromwell EA, Osborne JCP, Unnasch TR, Basáñez MG, Gass KM, Barbre KA, et al.
    PLoS Negl Trop Dis, 2021 07;15(7):e0008824.
    PMID: 34319976 DOI: 10.1371/journal.pntd.0008824
    Recent evidence suggests that, in some foci, elimination of onchocerciasis from Africa may be feasible with mass drug administration (MDA) of ivermectin. To achieve continental elimination of transmission, mapping surveys will need to be conducted across all implementation units (IUs) for which endemicity status is currently unknown. Using boosted regression tree models with optimised hyperparameter selection, we estimated environmental suitability for onchocerciasis at the 5 × 5-km resolution across Africa. In order to classify IUs that include locations that are environmentally suitable, we used receiver operating characteristic (ROC) analysis to identify an optimal threshold for suitability concordant with locations where onchocerciasis has been previously detected. This threshold value was then used to classify IUs (more suitable or less suitable) based on the location within the IU with the largest mean prediction. Mean estimates of environmental suitability suggest large areas across West and Central Africa, as well as focal areas of East Africa, are suitable for onchocerciasis transmission, consistent with the presence of current control and elimination of transmission efforts. The ROC analysis identified a mean environmental suitability index of 0·71 as a threshold to classify based on the location with the largest mean prediction within the IU. Of the IUs considered for mapping surveys, 50·2% exceed this threshold for suitability in at least one 5 × 5-km location. The formidable scale of data collection required to map onchocerciasis endemicity across the African continent presents an opportunity to use spatial data to identify areas likely to be suitable for onchocerciasis transmission. National onchocerciasis elimination programmes may wish to consider prioritising these IUs for mapping surveys as human resources, laboratory capacity, and programmatic schedules may constrain survey implementation, and possibly delaying MDA initiation in areas that would ultimately qualify.
  9. Fermentation of blueberry and blackberry juices using Lactobacillus plantarum, Streptococcus thermophilus and Bifidobacterium bifidum: Growth of probiotics, metabolism of phenolics, antioxidant capacity in vitro and sensory evaluation
    Wu Y, Li S, Tao Y, Li D, Han Y, Show PL, et al.
    Food Chem, 2021 Jun 30;348:129083.
    PMID: 33517000 DOI: 10.1016/j.foodchem.2021.129083
    In this study, three potential probiotic strains were selected to ferment blueberry and blackberry juices. The viable cell counts of selected strains were increased by 0.4-0.7 log CFU/mL in berry juices environments after 48-h fermentation. Meanwhile, the contents of cyanindin-3-glucoside and peonidin-3-glucoside decreased over 30%. Heatmap presented an upgrade trend of syringic acid, ferulic acid, gallic acid and lactic acid during fermentation. However, the contents of p-coumaric acid, protocatechuic acid, chlorogenic acid, critic acid and malic acid showed downgrade trend. The metabolism of phenolics probably contributed to the enhancement of the ABTS radical scavenging activity (40%-60%) in fermented berry juices. Moreover, the three strains presented different capacities on changing the quality of berry juices according to the PCA and LDA analysis. The contents of individual organic acids had positive correlations with sensory quality, especially for sourness. Overall, probiotic fermentation could improve the sensory quality of berry juices.
  10. Six new species of the spider genus Belisana/ (Araneae: Pholcidae) from Southeast Asia
    Zhu W, Li S
    Zootaxa, 2021 Apr 16;4963(1):zootaxa.4963.1.5.
    PMID: 33903565 DOI: 10.11646/zootaxa.4963.1.5
    Six new species belonging to Belisana Thorell, 1898 are described from Southeast Asia: Belisana bachma sp. nov. (Vietnam; male, female), B. cucphuong sp. nov. (Vietnam; male, female), B. jaegeri sp. nov. (Malaysia; male, female), B. kachin sp. nov. (Myanmar; male, female), B. putao sp. nov. (Myanmar; male) and B. tarang sp. nov. (Indonesia; male, female). These new species bring the total number of Belisana to 143 species worldwide.
  11. Effects of Blood Flow Restriction Training on Muscle Strength and Pain in Patients With Knee Injuries: A Meta-Analysis
    Li S, Shaharudin S, Abdul Kadir MR
    Am J Phys Med Rehabil, 2021 Apr 01;100(4):337-344.
    PMID: 33727516 DOI: 10.1097/PHM.0000000000001567
    BACKGROUND: Due to the pain caused by knee injuries, low-load resistance training with blood flow restriction (L-BFR) may be a potential adjuvant therapeutic tool in the rehabilitation of knee injuries. This review aimed to analyze the effectiveness of L-BFR training modality in knee rehabilitation.

    DESIGN: A meta-analysis was conducted to determine the potential impact of blood flow restriction on patients with knee injuries. PubMed, EBSCO, and Web of Science databases were searched for eligible studies from January 2000 until January 2020. The mean differences of the data were analyzed using Revman 5.3 software with a 95% confidence interval.

    RESULTS: Nine studies fulfilled the inclusion criteria. These studies involved 179 patients who received L-BFR, 96 patients who underwent high-load resistance training, and another 94 patients who underwent low-load resistance training. The analysis of pooled data showed that patients in both the L-BFR (standardized mean difference, 0.83 [0.53, 1.14], P < 0.01) and high-load resistance training (standardized mean difference, -0.09 [-0.43, 0.24], P = 0.58) groups experienced an increase in muscle strength after the training. In addition, pain score was significantly reduced in the L-BFR group compared with the other two groups (standardized mean difference, -0.61 [-1.19, -0.03], P = 0.04).

    CONCLUSIONS: Muscle strength increased after L-BFR and high-load resistance training compared with low-load resistance training. Furthermore, pain score was significantly reduced after L-BFR. Hence, L-BFR is a potential intervention to be applied in rehabilitation of knee injuries.

  12. Fulltext Apoptosis repressor with caspase recruitment domain (ARC) promotes bone regeneration of bone marrow-derived mesenchymal stem cells by activating Fgf-2/PI3K/Akt signaling
    Hu L, Wang Y, Pan H, Kadir K, Wen J, Li S, et al.
    Stem Cell Res Ther, 2021 03 16;12(1):185.
    PMID: 33726822 DOI: 10.1186/s13287-021-02253-5
    OBJECTIVES: This study aims to investigate whether apoptosis repressor with caspase recruitment domain (ARC) could promote survival and enhance osteogenic differentiation of bone marrow-derived mesenchymal stem cells (BMSCs).

    MATERIALS AND METHODS: The lentivirus transfection method was used to establish ARC-overexpressing BMSCs. The CCK-8 method was used to detect cell proliferation. The BD Pharmingen™ APC Annexin V Apoptosis Detection kit was used to detect cell apoptosis. The osteogenic capacity was investigated by OCN immunofluorescence staining, ALP analysis, ARS assays, and RT-PCR analysis. Cells were seeded into calcium phosphate cement (CPC) scaffolds and then inserted subcutaneously into nude mice and the defect area of the rat calvarium. Histological analysis was conducted to evaluate the in vivo cell apoptosis and new bone formation of the ARC-overexpressing BMSCs. RNA-seq was used to detect the possible mechanism of the effect of ARC on BMSCs.

    RESULTS: ARC promoted BMSC proliferation and inhibited cell apoptosis. ARC enhanced BMSC osteogenic differentiation in vitro. An in vivo study revealed that ARC can inhibit BMSC apoptosis and increase new bone formation. ARC regulates BMSCs mainly by activating the Fgf-2/PI3K/Akt pathway.

    CONCLUSIONS: The present study suggests that ARC is a powerful agent for promoting bone regeneration of BMSCs and provides a promising method for bone tissue engineering.

  13. Encapsulation of caffeine into starch matrices: Bitterness evaluation and suppression mechanism
    Shao M, Li S, Tan CP, Kraithong S, Gao Q, Fu X, et al.
    Int J Biol Macromol, 2021 Mar 15;173:118-127.
    PMID: 33444656 DOI: 10.1016/j.ijbiomac.2021.01.043
    In this study, caffeine (CA) was encapsulated into food-grade starch matrices, including swelled starch (SS), porous starch (PS), and V-type starch (VS). The bitterness of the microcapsules and suppression mechanisms were investigated using an electronic tongue, molecular dynamics (MD) simulation and the in vitro release kinetics of CA. All the CA-loaded microcapsules showed a lower bitterness intensity than the control. The MD results proved that the weak interactions between starch and CA resulted in a moderate CA release rate for SS-CA microcapsules. The PS-CA microcapsule presented the longest CA release, up to 40 min, whereas the VS-CA microcapsule completely released CA in 9 min. The CA release rate was found to be related to the microcapsule structure and rehydration properties. A low CA bitterness intensity could be attributed to a delay in the CA release rate and resistance to erosion of the microcapsules. The results of this work are valuable for improving starch-based microcapsules (oral-targeted drug-delivery systems) by suppressing the bitterness of alkaloid compounds.
  14. Molecular cloning and characterization of an atypical butyrylcholinesterase-like protein in zebrafish
    Tan KS, Zhang Y, Liu L, Li S, Zou X, Zeng W, et al.
    Comp Biochem Physiol B Biochem Mol Biol, 2021 03 02;255:110590.
    PMID: 33662568 DOI: 10.1016/j.cbpb.2021.110590
    Cholinesterases act as bio scavengers to clear organophosphorus (OP) compounds and prodrugs. The butyrylcholinesterase (BChE) gene has been found in several types of teleost fish but this gene has yet to be identified in cyprinid fish. Indeed, BChE homologs have not been found in the zebrafish (Danio rerio) genomic database. Here, we demonstrate that BChE activity is present in zebrafish, in line with other groups' findings. Using in-gel native-PAGE enzymatic activity staining and LC-MS/MS technique, an atypical BChE-like protein was identified in zebrafish. The si:ch211-93f2.1 gene was cloned, and His-tagged recombinant protein was expressed using the Pichia yeast system. The purified protein (molecular weight ~ 180 kDa) showed BChE activity, and degraded acetylcholinesterase (ACh) at a higher rate than BCh. However, phylogram analysis shows that this novel cholinesterase shared an evolutionary origin with carboxylic esterase rather than BChE. The zebrafish BChE-like protein shares structural characteristics with cholinesterase and carboxylesterase. The 2-arachidonoylglycerol (2-AG), nicosulfuron, and triacetin exhibited a higher binding affinity to the zebrafish BChE-like protein than BCh and ACh. With the identification of BChE-like protein in zebrafish, this study could shed light on the origin of BChE and may contribute towards the development of a BChE knockout zebrafish model for sensitive drug or toxin screening.
  15. Effects of descending or ascending stair exercise on body composition, insulin sensitivity, and inflammatory markers in young Chinese women with obesity: A randomized controlled trial
    Chow BC, Li S, Zhu X, Jiao J, Quach B, Baker JS, et al.
    J Sports Sci, 2021 Mar;39(5):496-502.
    PMID: 33012244 DOI: 10.1080/02640414.2020.1829362
    We examined the effects of descending (DSE) or ascending (ASE) stair exercise on body composition, insulin sensitivity, and inflammatory markers in young Chinese women with obesity. Thirty-six participants were randomly assigned into three groups DSE, ASE and a control group. The DSE and ASE groups performed three sessions of stair walking per week for 12 weeks with a gradual increase in repetitions. Following the exercise interventions, body composition related variables obtained by Dual-energy X-ray absorptiometry scans significantly decreased. Abdominal fat decreased in the DSE group only. Moreover, Insulin sensitivity improved significantly 3.5-fold in the DSE group compared with ASE group (insulin: -33.2% vs. -9.8%, homoeostasis model assessment for insulin resistance: -35.6% vs. -10.8%). Pro-inflammatory factors showed significant decreases in tumour necrosis factor-α (TNF-α) (-39.9% vs. -23.2%) for both intervention groups. The reduction in TNF-α concentrations in the DSE group was significantly different compared to the other two groups. Interleukin-6 significantly decreased in both exercise protocols. Our results show that 12-weeks induced stair walking improved body composition parameters in Chinese females with obesity. The results also demonstrate the superiority of the DSE protocol for improving insulin sensitivity. These findings may be attributable to the decreases observed in TNF- α levels.
  16. Fulltext Role of Snf-β in lipid accumulation in the high lipid-producing fungus Mucor circinelloides WJ11
    Nosheen S, Naz T, Yang J, Hussain SA, Fazili ABA, Nazir Y, et al.
    Microb Cell Fact, 2021 Feb 27;20(1):52.
    PMID: 33639948 DOI: 10.1186/s12934-021-01545-y
    BACKGROUND: Mucor circinelloides WJ11 is a high-lipid producing strain and an excellent producer of γ-linolenic acid (GLA) which is crucial for human health. We have previously identified genes that encode for AMP-activated protein kinase (AMPK) complex in M. circinelloides which is an important regulator for lipid accumulation. Comparative transcriptional analysis between the high and low lipid-producing strains of M. circinelloides showed a direct correlation in the transcriptional level of AMPK genes with lipid metabolism. Thus, the role of Snf-β, which encodes for β subunit of AMPK complex, in lipid accumulation of the WJ11 strain was evaluated in the present study.

    RESULTS: The results showed that lipid content of cell dry weight in Snf-β knockout strain was increased by 32 % (from 19 to 25 %). However, in Snf-β overexpressing strain, lipid content of cell dry weight was decreased about 25 % (from 19 to 14.2 %) compared to the control strain. Total fatty acid analysis revealed that the expression of the Snf-β gene did not significantly affect the fatty acid composition of the strains. However, GLA content in biomass was increased from 2.5 % in control strain to 3.3 % in Snf-β knockout strain due to increased lipid accumulation and decreased to 1.83 % in Snf-β overexpressing strain. AMPK is known to inactivate acetyl-CoA carboxylase (ACC) which catalyzes the rate-limiting step in lipid synthesis. Snf-β manipulation also altered the expression level of the ACC1 gene which may indicate that Snf-β control lipid metabolism by regulating ACC1 gene.

    CONCLUSIONS: Our results suggested that Snf-β gene plays an important role in regulating lipid accumulation in M. circinelloides WJ11. Moreover, it will be interesting to evaluate the potential of other key subunits of AMPK related to lipid metabolism. Better insight can show us the way to manipulate these subunits effectively for upscaling the lipid production. Up to our knowledge, it is the first study to investigate the role of Snf-β in lipid accumulation in M. circinelloides.

  17. Biochar from pyrolyzed Tibetan Yak dung as a novel additive in ensiling sweet sorghum: An alternate to the hazardous use of Yak dung as a fuel in the home
    Bai Y, Rafiq MK, Li S, Degen AA, Mašek O, Sun H, et al.
    J Hazard Mater, 2021 02 05;403:123647.
    PMID: 33264862 DOI: 10.1016/j.jhazmat.2020.123647
    Yak dung is used as fuel in Tibetan homes; however, this use is hazardous to health. An alternative use of the dung that would be profitable and offset the loss as a fuel would be very beneficial. Sweet sorghum silage with yak dung biochar as an additive was compared with a control silage with no additives and three silages with different commercial additives, namely Lactobacillus buchneri, Lactobacillus plantarum and Acremonium cellulase. Biochar-treated silage had a significantly greater concentration of water-soluble carbohydrates than the other silages (76 vs 12.4-45.8 g/kg DM) and a greater crude protein content (75.5 vs 61.4 g/kg DM), lactic acid concentration (40.7 vs 27.7 g/kg DM) and gross energy yield (17.8 vs 17.4 MJ/kg) than the control silage. Biochar-treated and control silages did not differ in in vitro digestibility and in total gas (507 vs 511 L/kg DM) and methane production (57.9 vs 57.1 L/kg DM). Biochar inhibited degradation of protein and water-soluble carbohydrates and enhanced lactic acid production, which improved storability of feed. It was concluded that yak dung biochar is an efficient, cost-effective ensiling additive. The profit could offset the loss of dung as fuel and improve the health of Tibetan people.
  18. DeepPSP: A Global-Local Information-Based Deep Neural Network for the Prediction of Protein Phosphorylation Sites
    Guo L, Wang Y, Xu X, Cheng KK, Long Y, Xu J, et al.
    J Proteome Res, 2021 01 01;20(1):346-356.
    PMID: 33241931 DOI: 10.1021/acs.jproteome.0c00431
    Identification of phosphorylation sites is an important step in the function study and drug design of proteins. In recent years, there have been increasing applications of the computational method in the identification of phosphorylation sites because of its low cost and high speed. Most of the currently available methods focus on using local information around potential phosphorylation sites for prediction and do not take the global information of the protein sequence into consideration. Here, we demonstrated that the global information of protein sequences may be also critical for phosphorylation site prediction. In this paper, a new deep neural network model, called DeepPSP, was proposed for the prediction of protein phosphorylation sites. In the DeepPSP model, two parallel modules were introduced to extract both local and global features from protein sequences. Two squeeze-and-excitation blocks and one bidirectional long short-term memory block were introduced into each module to capture effective representations of the sequences. Comparative studies were carried out to evaluate the performance of DeepPSP, and four other prediction methods using public data sets The F1-score, area under receiver operating characteristic curves (AUROC), and area under precision-recall curves (AUPRC) of DeepPSP were found to be 0.4819, 0.82, and 0.50, respectively, for S/T general site prediction and 0.4206, 0.73, and 0.39, respectively, for Y general site prediction. Compared with the MusiteDeep method, the F1-score, AUROC, and AUPRC of DeepPSP were found to increase by 8.6, 2.5, and 8.7%, respectively, for S/T general site prediction and by 20.6, 5.8, and 18.2%, respectively, for Y general site prediction. Among the tested methods, the developed DeepPSP method was also found to produce best results for different kinase-specific site predictions including CDK, mitogen-activated protein kinase, CAMK, AGC, and CMGC. Taken together, the developed DeepPSP method may offer a more accurate phosphorylation site prediction by including global information. It may serve as an alternative model with better performance and interpretability for protein phosphorylation site prediction.
  19. Fulltext Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1
    Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, et al.
    Autophagy, 2021 Jan;17(1):1-382.
    PMID: 33634751 DOI: 10.1080/15548627.2020.1797280
    In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
  20. Fulltext Evidence of Sex Differentiation Based on Morphological Traits During the Early Development Stage of Mud Crab Scylla paramamosain
    Cui W, Fang S, Lv L, Huang Z, Lin F, Wu Q, et al.
    Front Vet Sci, 2021;8:712942.
    PMID: 34395579 DOI: 10.3389/fvets.2021.712942
    In order to uncover the sexual difference in morphology and how early they appear during the development stage of mud crab Scylla paramamosain, we measured, observed, and biostatistically analyzed morphological traits related to sex. For unveiling the morphological differences between sexes, morphological traits involving abdomen width (AW), carapace length (CL), and carapace width (CW) were first measured during the crablet development stage of S. paramamosain in the present study. The correlation analyses and path analyses exhibited that sexual dimorphism in the third abdomen width (AW3) and fourth abdomen width (AW4) could be used for sex identification from stage C VI (stage VI of crablet). Based on the stepwise discriminant analysis and standardized traits, a sex discriminant equation was constructed, which is capable for sex identification in crablets from stage C VI. Observations for secondary sexual traits and abdomen morphology (shape and pleopods) using a dissecting microscope or scanning electron microscope indicated that sexes are easily identified at stage C VIII according to the abdomen shape; meanwhile, at stage C II based on pleopod difference, and at stage C I by the presence or absence of gonopores. The findings in this study contribute greatly to the accuracy of sex identification of S. paramamosain during the early development stage, which promotes the understanding of the morphological differentiation mechanism of sex.
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