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  1. Genetic differentiation for nuclear, mitochondrial and chloroplast genomes in common wild rice ( Oryza rufipogon Griff.) and cultivated rice ( Oryza sativa L.)
    Sun Q, Wang K, Yoshimura A, Doi K
    Theor Appl Genet, 2002 Jun;104(8):1335-1345.
    PMID: 12582589
    The genetic differentiation of nuclear, mitochondrial (mt) and chloroplast (cp) genomes was investigated by Southern and PCR analysis using 75 varieties of cultivated rice ( Oryza sativa L.) and 118 strains of common wild rice (CWR, Oryza rufipogon Griff.) from ten countries of Asia. The distinguishing differences between the Indica and Japonica cultivars were detected both in the nuclear genome and the cytoplasmic genome, confirming that the Indica-Japonica differentiation is of major importance for the three different classes of genome in cultivated rice. This differentiation was also detected in common wild rice with some differences among the genome compartments and the various regions. For nuclear DNA variation, both Indica-like and Japonica-like types were observed in the Chinese CWR, with the latter more-frequent than the former. No Japonica-like type was found in South Asia, and only two strains of the Japonica-like type were detected in Southeast Asia, thus the Indica-like type is the major type among South and Southeast Asian CWR. For mtDNA, only a few strains of the Japonica-like type were detected in CWR. For cpDNA, the Japonica type was predominant among the CWR strains from China, Bangladesh and Burma, while the Indica type was predominant among the CWR strains from Thailand, Malaysia, Cambodia and Sri Lanka, and both types were found in similar frequencies among the Indian CWR. Altogether, however, the degree of Indica-Japonica differentiation in common wild rice was much-less important than that in cultivated rice. Cluster analyses for nuclear and mitochondrial DNA variation revealed that some CWR strains showed large genetic distances from cultivated rice and formed clusters distinct from cultivated rice. Coincidence in the genetic differentiation between the three different classes of genome was much higher in cultivated rice than in CWR. Among the 75 cultivars, about 3/4 entries were "homoeotype" showing congruent results for nuclear, mt and cpDNA regarding the Indica-Japonica differentiation. In CWR, the proportions of homoeotypes were 5.7%, 15% and 48.8% in China, South Asia and Southeast Asia, respectively. Based on the average genetic distance among all the strains of CWR and cultivated rice for nuclear and mitochondrial genomes, the variability of the nuclear genome was found to be higher than that of the mitochondrial genome. The global pattern based on all genomes shows much-more diversification in CWR than that in cultivated rice.
  2. Ultrastructural change in lignocellulosic biomass during hydrothermal pretreatment
    Sun Q, Chen WJ, Pang B, Sun Z, Lam SS, Sonne C, et al.
    Bioresour Technol, 2021 Dec;341:125807.
    PMID: 34474237 DOI: 10.1016/j.biortech.2021.125807
    In recent years, visualization and characterization of lignocellulose at different scales elucidate the modifications of its ultrastructural and chemical features during hydrothermal pretreatment which include degradation and dissolving of hemicelluloses, swelling and partial hydrolysis of cellulose, melting and redepositing a part of lignin in the surface. As a result, cell walls are swollen, deformed and de-laminated from the adjacent layer, lead to a range of revealed droplets that appear on and within cell walls. Moreover, the certain extent morphological changes significantly promote the downstream processing steps, especially for enzymatic hydrolysis and anaerobic fermentation to bioethanol by increasing the contact area with enzymes. However, the formation of pseudo-lignin hinders the accessibility of cellulase to cellulose, which decreases the efficiency of enzymatic hydrolysis. This review is intended to bridge the gap between the microstructure studies and value-added applications of lignocellulose while inspiring more research prospects to enhance the hydrothermal pretreatment process.
  3. Accuracy of globe-sparing orbital reconstruction using individually bent titanium mesh: A comparative study
    Soh HY, Sun Q, Hu LH, Wang Y, Mao C, Peng X, et al.
    J Plast Reconstr Aesthet Surg, 2022 Jan 23.
    PMID: 35168922 DOI: 10.1016/j.bjps.2022.01.032
    Accurate reconstruction of orbital and midfacial defects following extensive globe-sparing maxillectomy is challenging, due to the complex anatomy of facial skeleton. The aim of this study is to evaluate the outcomes of individually bent titanium mesh in navigation-assisted reconstruction of post-ablative orbits in comparison with that without intraoperative navigation. Forty-one patients undergone globe-sparing maxillectomy and orbital floor reconstruction using individually bent titanium mesh with or without intraoperative navigation were assessed. Pre- and postoperative orbital projection and volume measurements were performed on both orbits. The unaffected orbit was used as a control for comparison. True-to-original orbital reconstruction was achieved in this study. The average difference of globe projection and orbital volume between unaffected and reconstructed orbits was 0.8 ± 0.5 mm and 0.9 ± 1.2cm3, respectively, in navigation-assisted group. In non-navigation-assisted group, the average difference of globe projection and orbital volume of unaffected and reconstructed orbit was 0.7 ± 0.5 mm and 1.3 ± 1.3cm3, respectively. There was no statistical significance in mean differences between unaffected and affected globe projection (P = 0.744) and orbital volume (P = 0.677) in both groups. There was also no significant difference observed when comparing the mean differences between pre- and postoperative globe projection (P = 0.659) and orbital volume (P = 0.582) in both groups. While intraoperative navigation system was shown to be effective in orbital reconstruction in the past decade, equal satisfactory post-ablative orbital reconstruction can be achieved with individually bent titanium mesh with or without intraoperative navigation.
  4. Fulltext To what extent do waste management strategies need adaptation to post-COVID-19?
    Mahyari KF, Sun Q, Klemeš JJ, Aghbashlo M, Tabatabaei M, Khoshnevisan B, et al.
    Sci Total Environ, 2022 Sep 01;837:155829.
    PMID: 35561899 DOI: 10.1016/j.scitotenv.2022.155829
    The world has been grappling with the crisis of the COVID-19 pandemic for more than a year. Various sectors have been affected by COVID-19 and its consequences. The waste management system is one of the sectors affected by such unpredictable pandemics. The experience of COVID-19 proved that adaptability to such pandemics and the post-pandemic era had become a necessity in waste management systems and this requires an accurate understanding of the challenges that have been arising. The accurate information and data from most countries severely affected by the pandemic are not still available to identify the key challenges during and post-COVID-19. The documented evidence from literature has been collected, and the attempt has been made to summarize the rising challenges and the lessons learned. This review covers all raised challenges concerning the various aspects of the waste management system from generation to final disposal (i.e., generation, storage, collection, transportation, processing, and burial of waste). The necessities and opportunities are recognized for increasing flexibility and adaptability in waste management systems. The four basic pillars are enumerated to adapt the waste management system to the COVID-19 pandemic and post-COVID-19 conditions. Striving to support and implement a circular economy is one of its basic strategies.
  5. Cobalt-Mediated Defect Engineering Endows High Reversible Amorphous VS4 Anode for Advanced Sodium-Ion Storage
    Zhang D, Shao Y, Wang J, Li Z, Wang Q, Sun H, et al.
    Small, 2024 Feb 01.
    PMID: 38299768 DOI: 10.1002/smll.202309901
    Metal sulfides are promising anode materials for sodium-ion batteries (SIBs) due to their structural diversity and high theoretical capacity, but the severe capacity decay and inferior rate capability caused by poor structural stability and sluggish kinetics impede their practical applications. Herein, a cobalt-doped amorphous VS4 wrapped by reduced graphene oxide (i.e., Co0.5 -VS4 /rGO) is developed through a Co-induced defect engineering strategy to boost the kinetics performances. The as-prepared Co0.5 -VS4 /rGO demonstrates excellent rate capacities over 10 A g-1 and superior cycling stability at 5 A g-1 over 1600 cycles, which is attributed to the defects formed by Co doping, the formed amorphous structure and the robust rGO substrate. The great features of Co0.5 -VS4 /rGO anode are further confirmed in sodium-ion capacitors when the active carbon cathode is used. Additionally, the relationships between metal doping, the derived defects, the amorphous structure, and the sodium storage of VS4 are uncovered. This work provides deep insights into preparing amorphous functional materials and also probes the potential applications of metal sulfide-based electrode materials for advanced batteries.
  6. Fulltext Molecular characterization of the viral structural protein genes in the first outbreak of dengue virus type 2 in Hunan Province, inland China in 2018
    Guan J, He Z, Qin M, Deng X, Chen J, Duan S, et al.
    BMC Infect Dis, 2021 Feb 10;21(1):166.
    PMID: 33568111 DOI: 10.1186/s12879-021-05823-3
    BACKGROUND: An unexpected dengue outbreak occurred in Hunan Province in 2018. This was the first dengue outbreak in this area of inland China, and 172 cases were reported.

    METHODS: To verify the causative agent of this outbreak and characterise the viral genes, the genes encoding the structural proteins C/prM/E of viruses isolated from local residents were sequenced followed by mutation and phylogenetic analysis. Recombination, selection pressure, potential secondary structure and three-dimensional structure analyses were also performed.

    RESULTS: Phylogenetic analysis revealed that all epidemic strains were of the cosmopolitan DENV-2 genotype and were most closely related to the Zhejiang strain (MH010629, 2017) and then the Malaysia strain (KJ806803, 2013). Compared with the sequence of DENV-2SS, 151 base substitutions were found in the sequences of 89 isolates; these substitutions resulted in 20 non-synonymous mutations, of which 17 mutations existed in all samples (two in the capsid protein, six in the prM/M proteins, and nine in the envelope proteins). Moreover, amino acid substitutions at the 602nd (E322:Q → H) and 670th (E390: N → S) amino acids may have enhanced the virulence of the epidemic strains. One new DNA binding site and five new protein binding sites were observed. Two polynucleotide binding sites and seven protein binding sites were lost in the epidemic strains compared with DENV-2SS. Meanwhile, five changes were found in helical regions. Minor changes were observed in helical transmembrane and disordered regions. The 429th amino acid of the E protein switched from a histamine (positively charged) to an asparagine (neutral) in all 89 isolated strains. No recombination events or positive selection pressure sites were observed. To our knowledge, this study is the first to analyse the genetic characteristics of epidemic strains in the first dengue outbreak in Hunan Province in inland China.

    CONCLUSIONS: The causative agent is likely to come from Zhejiang Province, a neighbouring province where dengue fever broke out in 2017. This study may help clarify the intrinsic geographical relatedness of DENV-2 and contribute to further research on pathogenicity and vaccine development.

  7. Fulltext Exosomes drive ferroptosis by stimulating iron accumulation to inhibit bacterial infection in crustaceans
    Sun Q, Yang J, Zhang M, Zhang Y, Ma H, Tran NT, et al.
    J Biol Chem, 2023 Dec;299(12):105463.
    PMID: 37977221 DOI: 10.1016/j.jbc.2023.105463
    Ferroptosis, characterized by iron-dependent cell death, has recently emerged as a critical defense mechanism against microbial infections. The present study aims to investigate the involvement of exosomes in the induction of ferroptosis and the inhibition of bacterial infection in crustaceans. Our findings provide compelling evidence for the pivotal role of exosomes in the immune response of crustaceans, wherein they facilitate intracellular iron accumulation and activate the ferroptotic pathways. Using RNA-seq and bioinformatic analysis, we demonstrate that cytochrome P450 (CYP) can effectively trigger ferroptosis. Moreover, by conducting an analysis of exosome cargo proteins, we have identified the participation of six-transmembrane epithelial antigen of prostate 4 in the regulation of hemocyte ferroptotic sensitivity. Subsequent functional investigations unveil that six-transmembrane epithelial antigen of prostate 4 enhances cellular Fe2+ levels, thereby triggering Fenton reactions and accelerating CYP-mediated lipid peroxidation, ultimately culminating in ferroptotic cell death. Additionally, the Fe2+-dependent CYP catalyzes the conversion of arachidonic acid into 20-hydroxyeicosatetraenoic acid, which activates the peroxisome proliferator-activated receptor. Consequently, the downstream target of peroxisome proliferator-activated receptor, cluster of differentiation 36, promotes intracellular fatty acid accumulation, lipid peroxidation, and ferroptosis. These significant findings shed light on the immune defense mechanisms employed by crustaceans and provide potential strategies for combating bacterial infections in this species.
  8. Construction of an Angular Tricyclic Benzofuran Skeleton Using the C-H Activation Strategy
    Sun Q, Guo F, Liu Y, Zhang Y, Zhang K, Wang Y, et al.
    J Org Chem, 2024 Mar 01;89(5):3304-3308.
    PMID: 38356371 DOI: 10.1021/acs.joc.3c02754
    A protocol for the construction of an angular tricyclic benzofuran skeleton based on the C-H activation strategy has been established. Different phthalide lactones on this skeleton can be easily assembled with various side chains by using C-H activation with aldehydes and subsequent reduction. This skeleton provides a versatile and crucial motif for the total synthesis of naturally occurring angular tricyclic benzofurans and their derivatives. Based on this protocol, the improved total syntheses of daldinin A and annullatin D were achieved in yields of 17.3 and 7.6%, respectively.
  9. Fulltext Agarose-resolvable InDel markers based on whole genome re-sequencing in cucumber
    Adedze YMN, Lu X, Xia Y, Sun Q, Nchongboh CG, Alam MA, et al.
    Sci Rep, 2021 02 16;11(1):3872.
    PMID: 33594240 DOI: 10.1038/s41598-021-83313-x
    Insertion and Deletion (InDel) are common features in genomes and are associated with genetic variation. The whole-genome re-sequencing data from two parents (X1 and X2) of the elite cucumber (Cucumis sativus) hybrid variety Lvmei No.1 was used for genome-wide InDel polymorphisms analysis. Obtained sequence reads were mapped to the genome reference sequence of Chinese fresh market type inbred line '9930' and gaps conforming to InDel were pinpointed. Further, the level of cross-parents polymorphism among five pairs of cucumber breeding parents and their corresponding hybrid varieties were used for evaluating hybrid seeds purity test efficiency of InDel markers. A panel of 48 cucumber breeding lines was utilized for PCR amplification versatility and phylogenetic analysis of these markers. In total, 10,470 candidate InDel markers were identified for X1 and X2. Among these, 385 markers with more than 30 nucleotide difference were arbitrary chosen. These markers were selected for experimental resolvability through electrophoresis on an Agarose gel. Two hundred and eleven (211) accounting for 54.81% of markers could be validated as single and clear polymorphic pattern while 174 (45.19%) showed unclear or monomorphic genetic bands between X1 and X2. Cross-parents polymorphism evaluation recorded 68 (32.23%) of these markers, which were designated as cross-parents transferable (CPT) InDel markers. Interestingly, the marker InDel114 presented experimental transferability between cucumber and melon. A panel of 48 cucumber breeding lines including parents of Lvmei No. 1 subjected to PCR amplification versatility using CPT InDel markers successfully clustered them into fruit and common cucumber varieties based on phylogenetic analysis. It is worth noting that 16 of these markers were predominately associated to enzymatic activities in cucumber. These agarose-based InDel markers could constitute a valuable resource for hybrid seeds purity testing, germplasm classification and marker-assisted breeding in cucumber.
  10. Fulltext Needs, gaps and opportunities for standard and e-mental health care among at-risk populations in the Asia Pacific in the context of COVID-19: a rapid scoping review
    Murphy JK, Khan A, Sun Q, Minas H, Hatcher S, Ng CH, et al.
    Int J Equity Health, 2021 07 12;20(1):161.
    PMID: 34253198 DOI: 10.1186/s12939-021-01484-5
    BACKGROUND: The COVID-19 pandemic is expected to have profound mental health impact, including in the Asia Pacific Economic Cooperation (APEC) region. Some populations might be at higher risk of experiencing negative mental health impacts and may encounter increased barriers to accessing mental health care. The pandemic and related restrictions have led to changes in care delivery, including a rapid shift to the use of e-mental health and digital technologies. It is therefore essential to consider needs and opportunities for equitable mental health care delivery to the most at-risk populations. This rapid scoping review: 1) identifies populations in the APEC region that are at higher risk of the negative mental health impacts of COVID-19, 2) identifies needs and gaps in access to standard and e-mental health care among these populations, and 3) explores the potential of e-mental health to address these needs.

    METHODS: We conducted a rapid scoping review following the PRISMA Extension for Scoping Reviews (PRISMA-ScR). We searched Medline, Embase and PsychInfo databases and Google Scholar using a search strategy developed in consultation with a biomedical librarian. We included records related to mental health or psychosocial risk factors and COVID-19 among at-risk groups; that referred to one or more APEC member economies or had a global, thus generalizable, scope; English language papers, and papers with full text available.

    RESULTS: A total of 132 records published between December 2019 and August 2020 were included in the final analysis. Several priority at-risk populations, risk factors, challenges and recommendations for standard and e-mental health care were identified. Results demonstrate that e-mental health care can be a viable option for care delivery but that specific accessibility and acceptability considerations must be considered. Options for in-person, hybrid or "low-tech" care must also remain available.

    CONCLUSIONS: The COVID-19 pandemic has highlighted the urgent need for equitable standard and e-mental health care. It has also highlighted the persistent social and structural inequities that contribute to poor mental health. The APEC region is vast and diverse; findings from the region can guide policy and practice in the delivery of equitable mental health care in the region and beyond.

  11. Hypoxia-inducible factor-1 alpha Correlates with Tumor-Associated Macrophages Infiltration, Influences Survival of Gastric Cancer Patients
    Zhang WJ, Chen C, Zhou ZH, Gao ST, Tee TJ, Yang LQ, et al.
    J Cancer, 2017;8(10):1818-1825.
    PMID: 28819379 DOI: 10.7150/jca.19057
    Background: Hypoxia was a common feature for accelerating tumor metastasis by both inducting epithelial-mesenchymal transition (EMT) of tumor cells and polarization of tumor-associated macrophages (TAMs). The association and roles between hypoxia, EMT and TAMs in the biological behavior of gastric cancer (GC) for the time being recurrence is unclear. Material and methods: hypoixa by expression of hypoxia-inducible factor-1 alpha (HIF-1α), polarized functional status of infiltrated TAMs by immunohistochemical staining of CD68 and CD163, and the expression of E-cadherin as EMT property had been evaluated in 236 patients consecutive with histologically confirmed GC. Clinical significance was assessed for all these patients. Results: High expression of HIF-1α was found in patients with aggressive features, especially for recurrent patients. High infiltration of TAMs and abnormal expression of EMT-marker were also related to aggressive characteristics and predicted poor prognosis in GC. Meanwwhile, there existed a significant correlation among expression of HIF-1α, infiltration of TAMs and EMT marker in GC tissues. Multivariate Cox analysis revealed that high expression of HIF-1α combined TAMs infiltration were independent prognostic factors for disease-specific survival rate. Conclusion: HIF-1α is an unfavorable indicator for prognosis, may promote tumor progression through the induction of EMT and establishment of a pro-tumor immunosuppressive microenvironment. Further investigation into the therapeutic effects of blocking hypoxia is possible a potential strategy for GC treatment.
  12. 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.
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