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Impact of DNA extraction methods on the observed microbial communities from the intestinal flora of the penaeid shrimp Litopenaeus vannamei

Jiang B, Sun J, Lv A, Hu X, Shi H, Sung Y, et al.

FEMS Microbiol Lett, 2019 05 01;366(9).
PMID: 31074797 DOI: 10.1093/femsle/fnz099

Two DNA extraction methods, the Zirmil-beating cell disruption method (ZBC) and the QIAamp fast DNA stool mini kit (QIA), were used to extract DNA from the intestinal flora of the penaeid shrimp Litopenaeus vannamei, and their microbial communities were analyzed using 16S rDNA high-throughput sequencing. Results were obtained in terms of the number of reads, alpha diversity indexes, beta diversity indexes and taxonomic composition. The alpha diversity indexes of the community, according to the ZBC method, were higher than those according to the QIA method. Furthermore, results from the three samples using the ZBC method were less consistent than those where the QIA method was used. Further, using the latter method led to substantive clustering. It is suggested that the QIA method is more stable and repeatable than the ZBC method. Although the two extraction methods shared the major abundant microflora based on 16S rDNA high-throughput sequencing, bias associated with diversity analysis indexes and certain species was observed.
Fulltext Maternal ancestry analyses of red tilapia strains based on D-loop sequences of seven tilapia populations

Jiang B, Fu J, Dong Z, Fang M, Zhu W, Wang L

PeerJ, 2019;7:e7007.
PMID: 31179190 DOI: 10.7717/peerj.7007

Background: Many tilapia species or varieties have been widely introduced and have become an economically important food fish in China. Information on the genetic backgrounds of these populations is deficient and requires more research, especially for red tilapia strains.
Methods: In the present study, displacement loop (D-loop) sequences were used to evaluate the genetic relationship and diversity of seven tilapia populations that are widely cultured in China; this was done specifically to speculate on the maternal ancestry of red tilapia strains. Three red tilapia varieties of Oreochromis ssp., Taiwan (TW), Israel (IL), and Malaysia (MY) strains and other populations, including O. aureus (AR), O. niloticus (NL), O. mossambicus (MS), and the GIFT strain of O. niloticus, were collected and analyzed in this study.
Results: A total of 146 polymorphic sites and 32 haplotypes of D-loop sequences were detected among 332 fish and four major haplotypes were shared among the populations. The TW and NL populations had a greater number of haplotypes (20 and 8, respectively). The haplotype diversity (Hd) and nucleotide diversity (π) of each population ranged from 0.234 to 0.826, and 0 to 0.060, respectively. The significant positive Tajima's D value of neutral test were detected in the NL, IL, and MY populations (P 0.05). The nearest K2P genetic distance (D = 0.014) was detected between the MS and TW populations, whereas, the farthest (D = 0.101) was found between the GIFT and AR populations. The results from the molecular variance analysis (AMOVA) showed that there was an extremely significant genetic variation observed among the populations (P
Factors associated with obesity: a case-control study of young adult Singaporean males

Shi H, Jiang B, Wei Sim JD, Chum ZZ, Ali NB, Toh MH

Mil Med, 2014 Oct;179(10):1158-65.
PMID: 25269135 DOI: 10.7205/MILMED-D-14-00064

A case-control study among Singapore Armed Forces' newly enlisted Servicemen was conducted to examine factors associated with male obesity. Four hundred and fifty-nine individuals from the Obese Basic Military Training program were selected as "cases" (average age: 19.5, body mass index: 30.4) and another 340 individuals were selected from the Normal Basic Military Training program as "controls" (average age: 19.3, body mass index: 21.4). Information such as family background, socioeconomic factors, and lifestyle practices were captured using facilitator-led questionnaires. Several variables were significantly associated with obesity after adjustments for possible confounders. These include childhood obesity (odds ratio [OR] = 2.06), less than an hour of exercise per day (OR = 2.97), Indian ethnicity (OR = 2.22), specific education backgrounds (especially that of Institute of Technical Education-OR = 2.75), father's employment at nonmanagerial/professional jobs (OR = 1.52), mother's employment at managerial/professional jobs (OR = 2.02), regular smoking (OR = 1.73) and alcohol consumption (OR = 2.26), 6 hours or less of sleep (OR = 3.73), obesity among family members (OR = 1.86 for mother; OR = 2.98 for siblings), parental history of diabetes mellitus (OR = 2.22 for father; OR = 2.70 for mother), and eating at inexpensive local food stalls (OR = 1.82). Our study found that a number of factors, ranging from personal and family backgrounds to lifestyle choices, were significantly associated with obesity among male youths.
Executive function measures of participants with mild cognitive impairment: Systematic review and meta-analysis of event-related potential studies

Che J, Cheng N, Jiang B, Liu Y, Liu H, Li Y, et al.

Int J Psychophysiol, 2024 Mar;197:112295.
PMID: 38266685 DOI: 10.1016/j.ijpsycho.2023.112295

OBJECTIVE: Objective measurements of executive functions using event-related potential (ERP) may be used as markers for differentiating healthy controls (HC) from patients with mild cognitive impairment (MCI). ERP is non-invasive, cost-effective, and affordable. Older adults with MCI demonstrate deteriorated executive function, serving as a potentially valid neurophysiological marker for identifying MCI. We aimed to review published ERP studies on executive function in older adults with MCI and summarize the performance differences by component between healthy older adults and older adults with MCI.
METHODS: Eight electronic databases (Web of Science, PubMed, ScienceDirect, American Psychological Association PsycNet, Cochrane Library, Scopus, Embase, and Ovid) were searched for the study. Articles published from January 1 to December 31, 2022, were considered for this review. A random-effects meta-analysis and between-study heterogeneity analysis were conducted using Comprehensive Meta-Analysis V3.0 software.
RESULTS: We identified 7829 articles of which 28 met the full inclusion criteria and were included in the systematic review and analyses. Our pooled analysis suggested that participants with MCI can be differentiated from HC by significant P200, P300, and N200 latencies. The P100 and P300 amplitudes were significantly smaller in participants with MCI when compared with those in the HCs, and the patients with MCI showed increased N200 amplitudes. Our findings provide new insights into potential electrophysiological biomarkers for diagnosing MCI.
Levels of Ancylostoma infections and phylogenetic analysis of cox 1 gene of A. ceylanicum in stray cat faecal samples from Guangzhou, China

Hu W, Yu XG, Wu S, Tan LP, Song MR, Abdulahi AY, et al.

J Helminthol, 2016 Jul;90(4):392-7.
PMID: 26123649 DOI: 10.1017/S0022149X15000413

Ancylostoma ceylanicum is a common zoonotic nematode. Cats act as natural reservoirs of the hookworm and are involved in transmitting infection to humans, thus posing a potential risk to public health. The prevalence of feline A. ceylanicum in Guangzhou (South China) was surveyed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). In total, 112 faecal samples were examined; 34.8% (39/112) and 43.8% (49/112) samples were positive with hookworms by microscopy and PCR method, respectively. Among them, 40.8% of samples harboured A. ceylanicum. Twelve positive A. ceylanicum samples were selected randomly and used for cox 1 sequence analysis. Sequencing results revealed that they had 97-99% similarity with A. ceylanicum cox 1 gene sequences deposited in GenBank. A phylogenetic tree showed that A. ceylanicum isolates were divided into two groups: one comprising four isolates from Guangzhou (South China), and the other comprising those from Malaysia, Cambodia and Guangzhou. In the latter group, all A. ceylanicum isolates from Guangzhou were clustered into a minor group again. The results indicate that the high prevalence of A. ceylanicum in stray cats in South China poses a potential risk of hookworm transmission from pet cats to humans, and that A. ceylanicum may be a species complex worldwide.
Hydrogen production and heavy metal immobilization using hyperaccumulators in supercritical water gasification

Su W, Liu P, Cai C, Ma H, Jiang B, Xing Y, et al.

J Hazard Mater, 2021 01 15;402:123541.
PMID: 32745873 DOI: 10.1016/j.jhazmat.2020.123541

The dispersion of hyperaccumulators used in the phytoremediation process has caused environmental concerns because of their heavy metal (HM) richness. It is important to reduce the environmental risks and prevent the HM to reenter the ecological cycle and thereby the human food web. In this work, supercritical water gasification (SCWG) technology was used to convert Sedum plumbizincicola into hydrogen (H2) gas and to immobilize HMs into biochar. The H2 production correlated with temperature ranging from 380 to 440 ℃ with the highest H2 yield of 2.74 mol/kg at 440 ℃. The free-radical reaction and steam reforming reaction at high temperatures were likely to be the mechanism behind the H2 production. The analyses of bio-oil by the Gas Chromatography-Mass Spectrometer (GC-MS) and Nuclear magnetic resonance spectroscopy (NMR) illustrated that the aromatic compounds, oxygenated compounds, and phenols were degraded into H2-rich gases. The increase of temperature enhanced the HM immobilization efficiency (>99.2 % immobilization), which was probably due to the quickly formed biochar that helped adsorb HMs. Then those HMs were chemically converted into stable forms through complexation with inorganic components on biochar, e.g., silicates, SiO2, and Al2O3. Consequently, the SCWG process was demonstrated as a promising approach for dispersing hyperaccumulators by immobilizing the hazardous HMs into biochar and simultaneously producing value-added H2-rich gases.
Fulltext Diverse genetic mechanisms underlie worldwide convergent rice feralization

Qiu J, Jia L, Wu D, Weng X, Chen L, Sun J, et al.

Genome Biol, 2020 03 26;21(1):70.
PMID: 32213201 DOI: 10.1186/s13059-020-01980-x

BACKGROUND: Worldwide feralization of crop species into agricultural weeds threatens global food security. Weedy rice is a feral form of rice that infests paddies worldwide and aggressively outcompetes cultivated varieties. Despite increasing attention in recent years, a comprehensive understanding of the origins of weedy crop relatives and how a universal feralization process acts at the genomic and molecular level to allow the rapid adaptation to weediness are still yet to be explored.
RESULTS: We use whole-genome sequencing to examine the origin and adaptation of 524 global weedy rice samples representing all major regions of rice cultivation. Weed populations have evolved multiple times from cultivated rice, and a strikingly high proportion of contemporary Asian weed strains can be traced to a few Green Revolution cultivars that were widely grown in the late twentieth century. Latin American weedy rice stands out in having originated through extensive hybridization. Selection scans indicate that most genomic regions underlying weedy adaptations do not overlap with domestication targets of selection, suggesting that feralization occurs largely through changes at loci unrelated to domestication.
CONCLUSIONS: This is the first investigation to provide detailed genomic characterizations of weedy rice on a global scale, and the results reveal diverse genetic mechanisms underlying worldwide convergent rice feralization.
Fulltext Binding of Duck Tembusu Virus Nonstructural Protein 2A to Duck STING Disrupts Induction of Its Signal Transduction Cascade To Inhibit Beta Interferon Induction

Zhang W, Jiang B, Zeng M, Duan Y, Wu Z, Wu Y, et al.

J Virol, 2020 04 16;94(9).
PMID: 32075929 DOI: 10.1128/JVI.01850-19

Duck Tembusu virus (DTMUV), which is similar to other mosquito-borne flaviviruses that replicate well in most mammalian cells, is an emerging pathogenic flavivirus that has caused epidemics in egg-laying and breeding waterfowl. Immune organ defects and neurological dysfunction are the main clinical symptoms of DTMUV infection. Preinfection with DTMUV makes the virus impervious to later interferon (IFN) treatment, revealing that DTMUV has evolved some strategies to defend against host IFN-dependent antiviral responses. Immune inhibition was further confirmed by screening for DTMUV-encoded proteins, which suggested that NS2A significantly inhibited IFN-β and IFN-stimulated response element (ISRE) promoter activity in a dose-dependent manner and facilitated reinfection with duck plague virus (DPV). DTMUV NS2A was able to inhibit duck retinoic acid-inducible gene-I (RIG-I)-, and melanoma differentiation-associated gene 5 (MDA5)-, mitochondrial-localized adaptor molecules (MAVS)-, stimulator of interferon genes (STING)-, and TANK-binding kinase 1 (TBK1)-induced IFN-β transcription, but not duck TBK1- and interferon regulatory factor 7 (IRF7)-mediated effective phases of IFN response. Furthermore, we found that NS2A competed with duTBK1 in binding to duck STING (duSTING), impaired duSTING-duSTING binding, and reduced duTBK1 phosphorylation, leading to the subsequent inhibition of IFN production. Importantly, we first identified that the W164A, Y167A, and S361A mutations in duSTING significantly impaired the NS2A-duSTING interaction, which is important for NS2A-induced IFN-β inhibition. Hence, our data demonstrated that DTMUV NS2A disrupts duSTING-dependent antiviral cellular defenses by binding with duSTING, which provides a novel mechanism by which DTMUV subverts host innate immune responses. The potential interaction sites between NS2A and duSTING may be the targets of future novel antiviral therapies and vaccine development.IMPORTANCE Flavivirus infections are transmitted through mosquitos or ticks and lead to significant morbidity and mortality worldwide with a spectrum of manifestations. Infection with an emerging flavivirus, DTMUV, manifests with clinical symptoms that include lesions of the immune organs and neurological dysfunction, leading to heavy egg drop and causing serious harm to the duck industry in China, Thailand, Malaysia, and other Southeast Asian countries. Mosquito cells, bird cells, and mammalian cell lines are all susceptible to DTMUV infection. An in vivo study revealed that BALB/c mice and Kunming mice were susceptible to DTMUV after intracerebral inoculation. Moreover, there are no reports about DTMUV-related human disease, but antibodies against DTMUV and viral RNA were detected in serum samples of duck industry workers. This information implies that DTMUV has expanded its host range and may pose a threat to mammalian health. However, the pathogenesis of DTMUV is largely unclear. Our results show that NS2A strongly blocks the STING-induced signal transduction cascade by binding with STING, which subsequently blocks STING-STING binding and TBK1 phosphorylation. More importantly, the W164, Y167, or S361 residues in duSTING were identified as important interaction sites between STING and NS2A that are vital for NS2A-induced IFN production and effective phases of IFN response. Uncovering the mechanism by which DTMUV NS2A inhibits IFN in the cells of its natural hosts, ducks, will help us understand the role of NS2A in DTMUV pathogenicity.
Fulltext Genomic insights into the evolution of Echinochloa species as weed and orphan crop

Wu D, Shen E, Jiang B, Feng Y, Tang W, Lao S, et al.

Nat Commun, 2022 02 03;13(1):689.
PMID: 35115514 DOI: 10.1038/s41467-022-28359-9

As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.