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Fruit characteristics, soluble sugar compositions and transcriptome analysis during the development of Citrus maxima "seedless", and identification of SUS and INV genes involved in sucrose degradation

Deng S, Mai Y, Niu J

Gene, 2019 Mar 20;689:131-140.
PMID: 30576805 DOI: 10.1016/j.gene.2018.12.016

Citrus maxima "seedless" is originally from Malaysia, and now is widely cultivated in Hainan province, China. The essential features of this cultivar are thin skin, green epicarp and seedless at the ripening stage. Here, using C. maxima "seedless" as experimental material, we investigated the physical and inclusion indicators, and found the accumulation of storage compounds during 120-210 DAF leading to inconsistent increase between volume and weight. Component analysis of soluble sugar indicated that arabinose and xylose have a high content in early development of pummelo juice sacs (PJS), whereas fructose, glucose and sucrose show a significant increase during PJS maturation. To clarify a global overview of the gene expressing profiles, the PJSs from four periods (60, 120, 180 and 240 DAF) were selected for comparative transcriptome analysis. The resulting 8275 unigenes showed differential expression during PJS development. Also, the stability of 11 housekeeping genes were evaluated by geNorm method, resulting in a set of five genes (UBC, ACT, OR23, DWA2 and CYP21D) used as control for normalization of gene expression. Based on transcriptome data, 5 sucrose synthases (SUSs) and 10 invertases (INVs) were identified to be involved in sucrose degradation. Importantly, SUS4 may be responsible for arabinose and xylose biosynthesis to form the cell wall in early development, while SUS3 and VIN2 may be important in the accumulation of soluble hexose leading to cell expansion through an osmotic-independent pathway in late development. The information provides valuable metabolite and genetic resources in C. maxima "seedless", and is important for achieving high fruit yield and quality.
An effective placental cotyledons proteins extraction method for 2D gel electrophoresis

Tan NJ, Daim LD, Jamil AA, Mohtarrudin N, Thilakavathy K

Electrophoresis, 2017 03;38(5):633-644.
PMID: 27992069 DOI: 10.1002/elps.201600377

Effective protein extraction is essential especially in producing a well-resolved proteome on 2D gels. A well-resolved placental cotyledon proteome, with good reproducibility, have allowed researchers to study the proteins underlying the physiology and pathophysiology of pregnancy. The aim of this study is to determine the best protein extraction protocol for the extraction of protein from placental cotyledons tissues for a two-dimensional gel electrophoresis (2D-GE). Based on widely used protein extraction strategies, 12 different extraction methodologies were carefully selected, which included one chemical extraction, two mechanical extraction coupled protein precipitations, and nine chemical extraction coupled protein precipitations. Extracted proteins were resolved in a one-dimensional gel electrophoresis and 2D-GE; then, it was compared with set criteria: extraction efficacy, protein resolution, reproducibility, and recovery efficiency. Our results revealed that a better profile was obtained by chemical extraction in comparison to mechanical extraction. We further compared chemical extraction coupled protein precipitation methodologies, where the DNase/lithium chloride-dense sucrose homogenization coupled dichloromethane-methanol precipitation (DNase/LiCl-DSH-D/MPE) method showed good protein extraction efficiency. This, however, was carried out with the best protein resolution and proteome reproducibility on 2D-gels. DNase/LiCl-DSH-D/MPE was efficient in the extraction of proteins from placental cotyledons tissues. In addition, this methodology could hypothetically allow the protein extraction of any tissue that contains highly abundant lipid and glycogen.
Fulltext A multi-objective path optimization method for plant protection robots based on improved A*-IWOA

Niu J, Shen C, Zhang L, Li Q, Ma H

PeerJ Comput Sci, 2024;10:e2620.
PMID: 39896365 DOI: 10.7717/peerj-cs.2620

BACKGROUND: The widespread adoption of plant protection robots has brought intelligent technology and agricultural machinery into deep integration. However, with advances in robotic autonomy, the energy that robots can carry remains limited due to constraints on battery capacity and weight. This limitation restricts the robots' ability to perform tasks continuously over extended periods.
METHODS: To address the challenges of achieving low energy consumption and efficiency in path planning for plant protection robots operating in mountainous environments, a multi-objective path optimization approach was developed. This approach combines the improved A* algorithm with the Improved Whale Optimization Algorithm (A*-IWOA), utilizing a 2.5D elevation grid map. First, an energy consumption model was created to account for the robot's energy use on slopes, based on its kinematic and dynamic models. Then, an improved A* search method was established by expanding to an 8-domain diagonal distance search and introducing a cost function influenced by cross-product decision values. Using the robot's motion trajectory as a constraint, the IWOA algorithm was applied to optimize the vector cross-product factor (p) by dynamically adjusting population positions and inertia weights, to minimize both energy consumption and path curvature. Finally, in simulation and orchard scenarios, the application effects of the proposed algorithm were evaluated and compared against notable variants of the A* algorithm using the robot ROS 2 operating system.
RESULTS: The experimental results show that the proposed algorithm substantially reduces the travel distance and enhances both path planning and computational efficiency. The improved approach meets the driving accuracy and energy consumption requirements for plant protection robots operating in mountainous environments.
DISCUSSION: This algorithm offers significant advantages in terms of computational accuracy, convergence speed, and efficiency. Moreover, the resulting paths satisfy the stringent energy consumption and path planning requirements of robots in unstructured mountain terrain. This improved algorithm could also be replicated and applied to other fields, such as picking robots, factory inspection robots, and complex industrial environments, where robust and efficient path planning is required.
Efficacy of Nigella sativa in alleviating benzo[a]pyrene-induced immunotoxicity in broilers

Latif IK, Karim AJ, Zuki AB, Zamri-Saad M, Niu JP, Noordin MM

Histol Histopathol, 2011 06;26(6):699-710.
PMID: 21472685 DOI: 10.14670/HH-26.699

The immune response of broiler chickens exposed to intra-tracheal (i.t.) administration of benzo[a]pyrene (BaP) with and without Nigella sativa (Ns) supplementation was investigated. A total of 120 day-old chicks were divided into four groups comprising 30 birds each, into a control, Ns, BaP, and BaP+Ns group. Immune responses to Newcastle disease (ND) were evaluated by haemagglutination inhibition (HI), phytohaemagglutinin (PHA) skin test and carbon clearance assay (CCA). In most instances, there was a significant increase (p<0.05) in the ND-HI antibody titers, PHA skin-swelling response and phagocytic activity in the BaP + Ns group compared to that of the BaP group. Likewise, organ weight and indices of the spleen, bursa of Fabricius and thymus of birds from the BaP + Ns group were also higher (p<0.05) than that of the BaP group from day 1 until day 21. It is concluded that exposure to BaP may exert adverse effects on the immune system of broilers which may increase their susceptibility to disease, and Ns supplementation significantly reduces these alterations.
Fulltext Pulmonary modulation of benzo[a]pyrene-induced hemato- and hepatotoxicity in broilers

Latif IK, Karim AJ, Zuki AB, Zamri-Saad M, Niu JP, Noordin MM

Poult Sci, 2010 Jul;89(7):1379-88.
PMID: 20548065 DOI: 10.3382/ps.2009-00622

Aftermath in several air pollution episodes with high concentrations of polycyclic aromatic hydrocarbons did not significantly affect health and performance of broilers despite its renowned sensitivity to polycyclic aromatic hydrocarbons. The aim of the study was to elucidate the previous lack of response in birds exposed to such severe episodes of air pollution. Benzo[a]pyrene (BaP) was used to simulate the influence of air pollution on hematology, selected organ function, and oxidative stress in broilers. One-day-old chicks were assigned to 5 equal groups composed of a control group, tricaprylin group, and 3 groups treated with BaP (at 1.5 microg, 150 microg, or 15 mg/kg of BW). The BaP was intratracheally administered to 1-d-old chicks for 5 consecutive days. The hematology, liver and kidney function, P450 activity, and malondialdehyde level especially in the group receiving 15 mg of BaP/kg of BW demonstrated evidence of hemato- and hepatoxicity via BaP-induced oxidative stress. The deleterious effect of exposure to high concentration of BaP in broiler chickens was probably due to the anatomy of this species and the half-life of BaP. Although the effect of BaP may be transient or irreversible, pathogen challenges faced during the period of suppression may prove fatal.
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.
Health benefits, mechanisms of interaction with food components, and delivery of tea polyphenols: a review

Niu J, Shang M, Li X, Sang S, Chen L, Long J, et al.

Crit Rev Food Sci Nutr, 2024;64(33):12487-12499.
PMID: 37665600 DOI: 10.1080/10408398.2023.2253542

Tea polyphenols (TPs) are the most important active component of tea and have become a research focus among natural products, thanks to their antioxidant, lipid-lowering, liver-protecting, anti-tumor, and other biological activities. Polyphenols can interact with other food components, such as protein, polysaccharides, lipids, and metal ions to further improve the texture, flavor, and sensory quality of food, and are widely used in food fields, such as food preservatives, antibacterial agents and food packaging. However, the instability of TPs under conditions such as light or heat and their low bioavailability in the gastrointestinal environment also hinder their application in food. In this review, we summarized the health benefits of TPs. In order to better use TPs in food, we analyzed the form and mechanism of interaction between TPs and main food components, such as polysaccharides and proteins. Moreover, we reviewed research into optimizing the applications of TPs in food by bio-based delivery systems, such as liposomes, nanoemulsions, and nanoparticles, so as to improve the stability and bioactivity of TPs in food application. As an effective active ingredient, TPs have great potential to be applied in functional food to produce benefits for human health.
Fulltext Real-world Effectiveness and Tolerability of Interferon-free Direct-acting Antiviral for 15,849 Patients with Chronic Hepatitis C: A Multinational Cohort Study

Ji F, Tran S, Ogawa E, Huang CF, Suzuki T, Wong YJ, et al.

J Clin Transl Hepatol, 2024 Jul 28;12(7):646-658.
PMID: 38993510 DOI: 10.14218/JCTH.2024.00089

BACKGROUND AND AIMS: As practice patterns and hepatitis C virus (HCV) genotypes (GT) vary geographically, a global real-world study from both East and West covering all GTs can help inform practice policy toward the 2030 HCV elimination goal. This study aimed to assess the effectiveness and tolerability of DAA treatment in routine clinical practice in a multinational cohort for patients infected with all HCV GTs, focusing on GT3 and GT6.
METHODS: We analyzed the sustained virological response (SVR12) of 15,849 chronic hepatitis C patients from 39 Real-World Evidence from the Asia Liver Consortium for HCV clinical sites in Asia Pacific, North America, and Europe between 07/01/2014-07/01/2021.
RESULTS: The mean age was 62±13 years, with 49.6% male. The demographic breakdown was 91.1% Asian (52.9% Japanese, 25.7% Chinese/Taiwanese, 5.4% Korean, 3.3% Malaysian, and 2.9% Vietnamese), 6.4% White, 1.3% Hispanic/Latino, and 1% Black/African-American. Additionally, 34.8% had cirrhosis, 8.6% had hepatocellular carcinoma (HCC), and 24.9% were treatment-experienced (20.7% with interferon, 4.3% with direct-acting antivirals). The largest group was GT1 (10,246 [64.6%]), followed by GT2 (3,686 [23.2%]), GT3 (1,151 [7.2%]), GT6 (457 [2.8%]), GT4 (47 [0.3%]), GT5 (1 [0.006%]), and untyped GTs (261 [1.6%]). The overall SVR12 was 96.9%, with rates over 95% for GT1/2/3/6 but 91.5% for GT4. SVR12 for GT3 was 95.1% overall, 98.2% for GT3a, and 94.0% for GT3b. SVR12 was 98.3% overall for GT6, lower for patients with cirrhosis and treatment-experienced (TE) (93.8%) but ≥97.5% for treatment-naive patients regardless of cirrhosis status. On multivariable analysis, advanced age, prior treatment failure, cirrhosis, active HCC, and GT3/4 were independent predictors of lower SVR12, while being Asian was a significant predictor of achieving SVR12.
CONCLUSIONS: In this diverse multinational real-world cohort of patients with various GTs, the overall cure rate was 96.9%, despite large numbers of patients with cirrhosis, HCC, TE, and GT3/6. SVR12 for GT3/6 with cirrhosis and TE was lower but still excellent (>91%).
acFibroMASH Index for the Diagnosis of Fibrotic MASH and Prediction of Liver-related Events: An International Multicenter Study

Feng G, Mózes FE, Ji D, Treeprasertsuk S, Okanoue T, Shima T, et al.

Clin Gastroenterol Hepatol, 2024 Oct 02.
PMID: 39362618 DOI: 10.1016/j.cgh.2024.07.045

BACKGROUND & AIMS: Metabolic dysfunction-associated steatohepatitis (MASH) and fibrotic MASH are significant health challenges. This multi-national study aimed to validate the acMASH index (including serum creatinine and aspartate aminotransferase concentrations) for MASH diagnosis and develop a new index (acFibroMASH) for non-invasively identifying fibrotic MASH and exploring its predictive value for liver-related events (LREs).
METHODS: We analyzed data from 3004 individuals with biopsy-proven metabolic dysfunction-associated steatotic liver disease (MASLD) across 29 Chinese and 9 international cohorts to validate the acMASH index and develop the acFibroMASH index. Additionally, we utilized the independent external data from a multi-national cohort of 9034 patients with MASLD to examine associations between the acFibroMASH index and the risk of LREs.
RESULTS: In the pooled global cohort, the acMASH index identified MASH with an area under the receiver operating characteristic curve (AUROC) of 0.802 (95% confidence interval [CI], 0.786-0.818). The acFibroMASH index (including the acMASH index plus liver stiffness measurement) accurately identified fibrotic MASH with an AUROC of 0.808 in the derivation cohort and 0.800 in the validation cohort. Notably, the AUROC for the acFibroMASH index was 0.835 (95% CI, 0.786-0.882), superior to that of the FAST score at 0.750 (95% CI, 0.693-0.800; P < .01) in predicting the 5-year risk of LREs. Patients with acFibroMASH >0.39 had a higher risk of LREs than those with acFibroMASH <0.15 (adjusted hazard ratio, 11.23; 95% CI, 3.98-31.66).
CONCLUSIONS: This multi-ethnic study validates the acMASH index as a reliable, noninvasive test for identifying MASH. The newly proposed acFibroMASH index is a reliable test for identifying fibrotic MASH and predicting the risk of LREs.