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The mitogenome of Pangasius sutchi (Teleostei, Siluriformes: Pangasiidae)

Zhao H, Kong X, Zhou C

Mitochondrial DNA, 2014 Oct;25(5):342-4.
PMID: 23795847 DOI: 10.3109/19401736.2013.800492

The Pangasius sutchi is an important ornamental and economic fish in Southeast Asia e.g. Thailand, Malaysia and China. The complete mitochondrial genome sequence of P. sutchi has been sequenced, which contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and a non-coding control region with the total length of 16,522 bp. The gene order and composition are similar to most of other vertebrates. Just like most other vertebrates, the bias of G and C was found in different region/genes statistics results. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. The mitogenome sequence of P. sutchi would contribute to better understand population genetics, evolution of this lineage.
Global, regional, and national burdens of depressive disorders in adolescents and young adults aged 10-24 years from 1990 to 2019: A trend analysis based on the Global Burden of Disease Study 2019

Luo J, Tang L, Kong X, Li Y

Asian J Psychiatr, 2024 Feb;92:103905.
PMID: 38262303 DOI: 10.1016/j.ajp.2023.103905

BACKGROUND: Depressive disorders (DD) including dysthymia and major depressive disorder (MDD) are common among adolescents and young adults. However, global trends in DD burden remain unclear.
METHODS: We analysed data from the Global Burden of Disease 2019 study on incidence, prevalence, disability-adjusted life years (DALYs), and mortality due to DD from 1990 to 2019 at global, regional and national levels.
RESULTS: Globally, dysthymia incidence increased notably in females, older age groups, and lower-middle income countries from 1990 to 2019. In contrast, MDD incidence decreased slightly over this period except in high-income North America. Females and middle-income countries had the highest dysthymia burden while North America had the highest MDD incidence and DALYs. Oman and Malaysia experienced largest increases in dysthymia and MDD burden respectively.
CONCLUSION: Despite certain global indicators suggesting a leveling off or decrease, it's clear that depressive disorders continue to be a significant and increasing issue, particularly among women, teenagers, and young adults. Differences between regions and countries indicate that specific interventions aimed at addressing economic inequalities, improving healthcare systems, and taking cultural factors into account could make a real difference in lessening the burden of depressive disorders. More research is needed to understand what's driving these trends so that we can develop better strategies for preventing and managing these conditions.
Fulltext Characterization of the complete plastid genome and phylogenetic analysis of Oreocharis argyreia var. angustifolia (Gesneriaceae)

Xu G, Li Z, Chen Z, Lee SY, Kong X

Mitochondrial DNA B Resour, 2023;8(10):1137-1140.
PMID: 37928400 DOI: 10.1080/23802359.2023.2270207

Oreocharis argyreia var. angustifolia of Gesneriaceae is widely distributed in South China, including Guangdong, Guangxi, Hunan, and Jiangxi provinces. However, genetic information of this species is limited, further contributing to the taxonomic complications surrounding this species. Thus, in this study, we assembled and characterized the complete chloroplast genome of O. argyreia var. angustifolia as a genomic resource for future studies. The complete plastid genome was 154,675 bp in size, with a pair of inverted repeat regions of 25,329 bp each, separating the 85,977-bp large and 18,040-bp small single copy regions. A total of 131 genes were predicted, consisting of 86 protein-coding, 37 tRNA, and eight rRNA genes. The overall GC content was 37.6%. Phylogenetic analysis based on 79 shared unique CDS resulted in a fully resolved phylogenetic tree using both the maximum likelihood and Bayesian inference methods. Based on current circumscription, both methods indicated that Oreocharis is monophyletic; O. argyreia var. angustifolia diverged after O. chienii, which then followed by the divergence of the other three species included namely, O. continifolia, O. esquirolii, and O. mileensis. The genomic data obtained will be useful for future studies on the phylogenetics and evolution of Gesneriaceae.
Fulltext Molecular epidemiology demonstrates that imported and local strains circulated during the 2014 dengue outbreak in Guangzhou, China

Li G, Pan P, He Q, Kong X, Wu K, Zhang W, et al.

Virol Sin, 2017 Feb;32(1):63-72.
PMID: 28120220 DOI: 10.1007/s12250-016-3872-8

The dengue virus (DENV) is a vital global public health issue. The 2014 dengue epidemic in Guangzhou, China, caused approximately 40,000 cases of infection and five deaths. We carried out a comprehensive investigation aimed at identifying the transmission sources in this dengue epidemic. To analyze the phylogenetics of the 2014 dengue strains, the envelope (E) gene sequences from 17 viral strains isolated from 168 dengue patient serum samples were sequenced and a phylogenetic tree was reconstructed. All 17 strains were serotype I strains, including 8 genotype I and 9 genotype V strains. Additionally, 6 genotype I strains that were probably introduced to China from Thailand before 2009 were widely transmitted in the 2013 and 2014 epidemics, and they continued to circulate until 2015, with one affinis strain being found in Singapore. The other 2 genotype I strains were introduced from the Malaya Peninsula in 2014. The transmission source of the 9 genotype V strains was from Malaysia in 2014. DENVs of different serotypes and genotypes co-circulated in the 2014 dengue outbreak in Guangzhou. Moreover, not only had DENV been imported to Guangzhou, but it had also been gradually exported, as the viruses exhibited an enzootic transmission cycle in Guangzhou.
Glomerular Filtration Rates in Asians

Teo BW, Zhang L, Guh JY, Tang SCW, Jha V, Kang DH, et al.

Adv Chronic Kidney Dis, 2018 01;25(1):41-48.
PMID: 29499886 DOI: 10.1053/j.ackd.2017.10.005

The National Kidney Foundation Kidney Disease Outcomes Quality Initiative guidelines recommended the Modification of Diet in Renal Disease study equation for estimating glomerular filtration rate (GFR) for the classification of CKD, but its accuracy was limited to North American patients with estimated GFR <60 mL/min per 1.73 m2 body surface area of European (White) or African (Black) descent. The Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) developed another equation for estimating GFR, derived from a population that included both participants without kidney disease and with CKD. But many ethnicities were inadequately represented. The International Society of Nephrology, Kidney Disease Improving Global Outcomes committee promulgated clinical practice guidelines, which recommended the CKD-EPI equation. Investigators in Asia subsequently assessed the performance of these GFR estimating equations-the Modification of Diet in Renal Disease study equation, the CKD-EPI equation (creatinine only), and the CKD-EPI equations (creatinine and cystatin C). In this review, we summarize the studies performed in Asia on validating or establishing new Asian ethnicity GFR estimating equations. We included both prospective and retrospective studies which used serum markers traceable to reference materials and focused the review of the performance of GFR estimation by comparisons with the GFR estimations obtained from the CKD-EPI equations.
Reassortment and genomic analysis of a G9P[8]-E2 rotavirus isolated in China

Peng R, Li D, Wang J, Xiong G, Wang M, Liu D, et al.

Virol J, 2023 Jun 22;20(1):135.
PMID: 37349792 DOI: 10.1186/s12985-023-02064-5

OBJECTIVE: To isolate a prevalent G9P[8] group A rotavirus (RVA) (N4006) in China and investigate its genomic and evolutionary characteristics, with the goal of facilitating the development of a new rotavirus vaccine.
METHODS: The RVA G9P[8] genotype from a diarrhea sample was passaged in MA104 cells. The virus was evaluated by TEM, polyacrylamide gel electrophoresis, and indirect immunofluorescence assay. The complete genome of virus was obtained by RT-PCR and sequencing. The genomic and evolutionary characteristics of the virus were evaluated by nucleic acid sequence analysis with MEGA ver. 5.0.5 and DNASTAR software. The neutralizing epitopes of VP7 and VP4 (VP5* and VP8*) were analyzed using BioEdit ver. 7.0.9.0 and PyMOL ver. 2.5.2.
RESULTS: The RVA N4006 (G9P[8] genotype) was adapted in MA104 cells with a high titer (105.5 PFU/mL). Whole-genome sequence analysis showed N4006 to be a reassortant rotavirus of Wa-like G9P[8] RVA and the NSP4 gene of DS-1-like G2P[4] RVA, with the genotype constellation G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 (G9P[8]-E2). Phylogenetic analysis indicated that N4006 had a common ancestor with Japanese G9P[8]-E2 rotavirus. Neutralizing epitope analysis showed that VP7, VP5*, and VP8* of N4006 had low homology with vaccine viruses of the same genotype and marked differences with vaccine viruses of other genotypes.
CONCLUSION: The RVA G9P[8] genotype with the G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 (G9P[8]-E2) constellation predominates in China and may originate from reassortment between Japanese G9P[8] with Japanese DS-1-like G2P[4] rotaviruses. The antigenic variation of N4006 with the vaccine virus necessitates an evaluation of the effect of the rotavirus vaccine on G9P[8]-E2 genotype rotavirus.
Whole-transcriptome analysis reveals mechanisms underlying antibacterial activity and biofilm inhibition by a malic acid combination (MAC) in Pseudomonas aeruginosa

Song K, Chen L, Suo N, Kong X, Li J, Wang T, et al.

PeerJ, 2023;11:e16476.
PMID: 38084141 DOI: 10.7717/peerj.16476

BACKGROUND: Pseudomonas aeruginosa is a highly prevalent bacterial species known for its ability to cause various infections and its remarkable adaptability and biofilm-forming capabilities. In earlier work, we conducted research involving the screening of 33 metabolites obtained from a commercial source against two prevalent bacterial strains, Escherichia coli and Staphylococcus aureus. Through screening assays, we discovered a novel malic acid combination (MAC) consisting of malic acid, citric acid, glycine, and hippuric acid, which displayed significant inhibitory effects. However, the precise underlying mechanism and the potential impact of the MAC on bacterial biofilm formation remain unknown and warrant further investigation.
METHODS: To determine the antibacterial effectiveness of the MAC against Pseudomonas aeruginosa, we conducted minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) assays. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) techniques were employed to observe bacterial morphology and biofilm formation. We further performed a biofilm inhibition assay to assess the effect of the MAC on biofilm formation. Whole-transcriptome sequencing and bioinformatics analysis were employed to elucidate the antibacterial mechanism of the MAC. Additionally, the expression levels of differentially expressed genes were validated using the real-time PCR approach.
RESULTS: Our findings demonstrated the antibacterial activity of the MAC against P. aeruginosa. SEM analysis revealed that the MAC can induce morphological changes in bacterial cells. The biofilm assay showed that the MAC could reduce biofilm formation. Whole-transcriptome analysis revealed 1093 differentially expressed genes consisting of 659 upregulated genes and 434 downregulated genes, in response to the MAC treatment. Mechanistically, the MAC inhibited P. aeruginosa growth by targeting metabolic processes, secretion system, signal transduction, and cell membrane functions, thereby potentially compromising the survival of this human pathogen. This study provides valuable insights into the antibacterial and antibiofilm activities of the MAC, a synergistic and cost-effective malic acid combination, which holds promise as a potential therapeutic drug cocktail for treating human infectious diseases in the future.
Fulltext Multi-platform discovery of haplotype-resolved structural variation in human genomes

Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, et al.

Nat Commun, 2019 04 16;10(1):1784.
PMID: 30992455 DOI: 10.1038/s41467-018-08148-z

The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs (≥50 bp) per genome. We also discover 156 inversions per genome and 58 of the inversions intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a three to sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The methods and the dataset presented serve as a gold standard for the scientific community allowing us to make recommendations for maximizing structural variation sensitivity for future genome sequencing studies.