Displaying publications 81 - 100 of 149 in total

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  1. Yang X, Ikhwanuddin M, Li X, Lin F, Wu Q, Zhang Y, et al.
    Mar Biotechnol (NY), 2018 Feb;20(1):20-34.
    PMID: 29152671 DOI: 10.1007/s10126-017-9784-2
    The molecular mechanism underlying sex determination and gonadal differentiation of the mud crab (Scylla paramamosain) has received considerable attention, due to the remarkably biological and economic differences between sexes. However, sex-biased genes, especially non-coding genes, which account for these differences, remain elusive in this crustacean species. In this study, the first de novo gonad transcriptome sequencing was performed to identify both differentially expressed genes and long non-coding RNAs (lncRNAs) between male and female S. paramamosain by using Illumina Hiseq2500. A total of 79,282,758 and 79,854,234 reads were generated from ovarian and testicular cDNA libraries, respectively. After filtrating and de novo assembly, 262,688 unigenes were produced from both libraries. Of these unigenes, 41,125 were annotated with known protein sequences in public databases. Homologous genes involved in sex determination and gonadal development pathways (Sxl-Tra/Tra-2-Dsx/Fru, Wnt4, thyroid hormone synthesis pathway, etc.) were identified. Three hundred and sixteen differentially expressed unigenes were further identified between both transcriptomes. Meanwhile, a total of 233,078 putative lncRNAs were predicted. Of these lncRNAs, 147 were differentially expressed between sexes. qRT-PCR results showed that nine lncRNAs negatively regulated the expression of eight genes, suggesting a potential role in sex differentiation. These findings will provide fundamental resources for further investigation on sex differentiation and regulatory mechanism in crustaceans.
  2. Wu Q, Miao G, Li X, Liu W, Ikhwanuddin M, Ma H
    Mol Biol Rep, 2018 Dec;45(6):1913-1918.
    PMID: 30203240 DOI: 10.1007/s11033-018-4339-9
    The blue swimming crab (Portunus pelagicus) is a valuable marine fishery resource in Indo-West Pacific Ocean. So far, rare genetic resource of this species is available. In this report, the restriction-site associated DNA (RAD) approach was employed to mine the genomic information and identify molecular markers in P. pelagicus. A total of 0.82 Gbp clean data were generated from the genome of individual "X2A". De novo assembly produced 85,796 contigs with an average length of 339 bp. A total of 45,464 putative SNPs and 17,983 microsatellite loci were identified from the genomes of ten individuals. Furthermore, 31 pairs of primers were successfully designed, with 16 of them exhibiting polymorphism in a wild population. For these polymorphic loci, the expected and observed alleles per locus ranged from 1.064 to 7.314 and from 2 to 11, respectively. The expected and observed heterozygosity per locus ranged from 0.0615 to 0.819 and from 0.0626 to 1.000, respectively. Nine loci showed high informative with polymorphism information content (PIC) > 0.5. Five loci significantly deviated from Hardy-Weinberg equilibrium in the samples analyzed. No linkage disequilibrium was found among the 16 polymorphic microsatellite loci. This study provided massive genetic resource and polymorphic molecular markers that should be helpful for studies on conservation genetics, population dynamics and genetic diversity of P. pelagicus and related crab species.
  3. Li X, Hussain SA, Sobri S, Md Said MS
    Chemosphere, 2021 May;271:129502.
    PMID: 33465622 DOI: 10.1016/j.chemosphere.2020.129502
    Most developing countries in the world face the common challenges of reducing air pollution and advancing the process of sustainable development, especially in China. Air pollution research is a complex system and one of the main methods is through numerical simulation. The air quality model is an important technical method, it allows researchers to better analyze air pollutants in different regions. In addition, the SCB is a high-humidity and foggy area, and the concentration of atmospheric pollutants is always high. However, research on this region, one of the four most polluted regions in China, is still lacking. Reviewing the application of air quality models in the SCB air pollution has not been reported thoroughly. To fill these gaps, this review provides a comprehensive narration about i) The status of air pollution in SCB; ii) The application of air quality models in SCB; iii) The problems and application prospects of air quality models in the research of air pollution. This paper may provide a theoretical reference for the prevention and control of air pollution in the SCB and other heavily polluted areas in China and give some1inspirations for air pollution forecast in other countries with complex terrain.
  4. Porwal P, Pachade S, Kokare M, Deshmukh G, Son J, Bae W, et al.
    Med Image Anal, 2020 01;59:101561.
    PMID: 31671320 DOI: 10.1016/j.media.2019.101561
    Diabetic Retinopathy (DR) is the most common cause of avoidable vision loss, predominantly affecting the working-age population across the globe. Screening for DR, coupled with timely consultation and treatment, is a globally trusted policy to avoid vision loss. However, implementation of DR screening programs is challenging due to the scarcity of medical professionals able to screen a growing global diabetic population at risk for DR. Computer-aided disease diagnosis in retinal image analysis could provide a sustainable approach for such large-scale screening effort. The recent scientific advances in computing capacity and machine learning approaches provide an avenue for biomedical scientists to reach this goal. Aiming to advance the state-of-the-art in automatic DR diagnosis, a grand challenge on "Diabetic Retinopathy - Segmentation and Grading" was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI - 2018). In this paper, we report the set-up and results of this challenge that is primarily based on Indian Diabetic Retinopathy Image Dataset (IDRiD). There were three principal sub-challenges: lesion segmentation, disease severity grading, and localization of retinal landmarks and segmentation. These multiple tasks in this challenge allow to test the generalizability of algorithms, and this is what makes it different from existing ones. It received a positive response from the scientific community with 148 submissions from 495 registrations effectively entered in this challenge. This paper outlines the challenge, its organization, the dataset used, evaluation methods and results of top-performing participating solutions. The top-performing approaches utilized a blend of clinical information, data augmentation, and an ensemble of models. These findings have the potential to enable new developments in retinal image analysis and image-based DR screening in particular.
  5. Park S, Saw SN, Li X, Paknezhad M, Coppola D, Dinish US, et al.
    Biomed Opt Express, 2021 Jun 01;12(6):3671-3683.
    PMID: 34221687 DOI: 10.1364/BOE.415105
    Atopic dermatitis (AD) is a skin inflammatory disease affecting 10% of the population worldwide. Raster-scanning optoacoustic mesoscopy (RSOM) has recently shown promise in dermatological imaging. We conducted a comprehensive analysis using three machine-learning models, random forest (RF), support vector machine (SVM), and convolutional neural network (CNN) for classifying healthy versus AD conditions, and sub-classifying different AD severities using RSOM images and clinical information. CNN model successfully differentiates healthy from AD patients with 97% accuracy. With limited data, RF achieved 65% accuracy in sub-classifying AD patients into mild versus moderate-severe cases. Identification of disease severities is vital in managing AD treatment.
  6. Harreld JH, Mohammed N, Goldsberry G, Li X, Li Y, Boop F, et al.
    AJNR Am J Neuroradiol, 2015 May;36(5):993-9.
    PMID: 25614472 DOI: 10.3174/ajnr.A4221
    Postoperative intraspinal subdural collections in children after posterior fossa tumor resection may temporarily hinder metastasis detection by MR imaging or CSF analysis, potentially impacting therapy. We investigated the incidence, imaging and clinical features, predisposing factors, and time course of these collections after posterior fossa tumor resection.
  7. Miller V, Jenkins DA, Dehghan M, Srichaikul K, Rangarajan S, Mente A, et al.
    Lancet Diabetes Endocrinol, 2024 May;12(5):330-338.
    PMID: 38588684 DOI: 10.1016/S2213-8587(24)00069-X
    BACKGROUND: The association between the glycaemic index and the glycaemic load with type 2 diabetes incidence is controversial. We aimed to evaluate this association in an international cohort with diverse glycaemic index and glycaemic load diets.

    METHODS: The PURE study is a prospective cohort study of 127 594 adults aged 35-70 years from 20 high-income, middle-income, and low-income countries. Diet was assessed at baseline using country-specific validated food frequency questionnaires. The glycaemic index and the glycaemic load were estimated on the basis of the intake of seven categories of carbohydrate-containing foods. Participants were categorised into quintiles of glycaemic index and glycaemic load. The primary outcome was incident type 2 diabetes. Multivariable Cox Frailty models with random intercepts for study centre were used to calculate hazard ratios (HRs).

    FINDINGS: During a median follow-up of 11·8 years (IQR 9·0-13·0), 7326 (5·7%) incident cases of type 2 diabetes occurred. In multivariable adjusted analyses, a diet with a higher glycaemic index was significantly associated with a higher risk of diabetes (quintile 5 vs quintile 1; HR 1·15 [95% CI 1·03-1·29]). Participants in the highest quintile of the glycaemic load had a higher risk of incident type 2 diabetes compared with those in the lowest quintile (HR 1·21, 95% CI 1·06-1·37). The glycaemic index was more strongly associated with diabetes among individuals with a higher BMI (quintile 5 vs quintile 1; HR 1·23 [95% CI 1·08-1·41]) than those with a lower BMI (quintile 5 vs quintile 1; 1·10 [0·87-1·39]; p interaction=0·030).

    INTERPRETATION: Diets with a high glycaemic index and a high glycaemic load were associated with a higher risk of incident type 2 diabetes in a multinational cohort spanning five continents. Our findings suggest that consuming low glycaemic index and low glycaemic load diets might prevent the development of type 2 diabetes.

    FUNDING: Full funding sources are listed at the end of the Article.

  8. Zhang Z, Hu Y, Ji H, Lin Q, Li X, Sang S, et al.
    Food Chem, 2023 Jul 30;415:135736.
    PMID: 36863232 DOI: 10.1016/j.foodchem.2023.135736
    Core-shell biopolymer nanoparticles are assembled from a hydrophobic protein (zein) core and a hydrophilic polysaccharide (carboxymethyl dextrin) shell. The nanoparticles were shown to have good stability and the ability to protect quercetin from chemical degradation under long-term storage, pasteurization, and UV irradiation. Spectroscopy analysis shows that electrostatic, hydrogen bonding, and hydrophobic interactions are the main driving forces for the formation of composite nanoparticles. Quercetin coated with nanoparticles significantly enhanced its antioxidant and antibacterial activities and showed good stability and slow release in vitro during simulated gastrointestinal digestion. Furthermore, the encapsulation efficiency of carboxymethyl dextrin-coated zein nanoparticles (81.2%) for quercetin was significantly improved compared with that of zein nanoparticles alone (58.4%). These results indicate that carboxymethyl dextrin-coated zein nanoparticles can significantly improve the bioavailability of hydrophobic nutrient molecules such as quercetin and provide a valuable reference for their application in the field of biological delivery of energy drinks and food.
  9. Yin W, Yan R, Zhou X, Li X, Sang S, Julian McClements D, et al.
    Food Chem, 2023 Mar 24;419:136004.
    PMID: 37054511 DOI: 10.1016/j.foodchem.2023.136004
    Chitosan (CS) films have poor mechanical property, low water-resistance and limited antimicrobial activity, which hinder their application in food preservation industry. Cinnamaldehyde-tannic acid-zinc acetate nanoparticles (CTZA NPs) assembled from edible medicinal plant extracts were successfully incorporated into CS films to solve these issues. The tensile strength and water contact angle of the composite films increased about 5.25-fold and 17.55°. The addition of CTZA NPs reduced the water sensitivity of CS films, which could undergo appreciable stretching in water without breaking. Furthermore, CTZA NPs significantly enhanced the UV adsorption, antibacterial, and antioxidant properties of the films, while reduced their water vapor permeability. Moreover, it was possible to print inks onto the films because the presence of the hydrophobic CTZA NPs facilitated the deposition of carbon powder onto their surfaces. The films with great antibacterial and antioxidant activities can be applied for food packaging application.
  10. Niu J, Shang M, Li X, Sang S, Chen L, Long J, et al.
    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.
  11. Jahangir CA, Page DB, Broeckx G, Gonzalez CA, Burke C, Murphy C, et al.
    J Pathol, 2024 Mar;262(3):271-288.
    PMID: 38230434 DOI: 10.1002/path.6238
    Recent advances in the field of immuno-oncology have brought transformative changes in the management of cancer patients. The immune profile of tumours has been found to have key value in predicting disease prognosis and treatment response in various cancers. Multiplex immunohistochemistry and immunofluorescence have emerged as potent tools for the simultaneous detection of multiple protein biomarkers in a single tissue section, thereby expanding opportunities for molecular and immune profiling while preserving tissue samples. By establishing the phenotype of individual tumour cells when distributed within a mixed cell population, the identification of clinically relevant biomarkers with high-throughput multiplex immunophenotyping of tumour samples has great potential to guide appropriate treatment choices. Moreover, the emergence of novel multi-marker imaging approaches can now provide unprecedented insights into the tumour microenvironment, including the potential interplay between various cell types. However, there are significant challenges to widespread integration of these technologies in daily research and clinical practice. This review addresses the challenges and potential solutions within a structured framework of action from a regulatory and clinical trial perspective. New developments within the field of immunophenotyping using multiplexed tissue imaging platforms and associated digital pathology are also described, with a specific focus on translational implications across different subtypes of cancer. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
  12. Lou Z, Xu Y, Xiang K, Su N, Qin L, Li X, et al.
    FEBS J, 2006 Oct;273(19):4538-47.
    PMID: 16972940
    The Nipah and Hendra viruses are highly pathogenic paramyxoviruses that recently emerged from flying foxes to cause serious disease outbreaks in humans and livestock in Australia, Malaysia, Singapore and Bangladesh. Their unique genetic constitution, high virulence and wide host range set them apart from other paramyxoviruses. These characteristics have led to their classification into the new genus Henpavirus within the family Paramyxoviridae and to their designation as Biosafety Level 4 pathogens. The fusion protein, an enveloped glycoprotein essential for viral entry, belongs to the family of class I fusion proteins and is characterized by the presence of two heptad repeat (HR) regions, HR1 and HR2. These two regions associate to form a fusion-active hairpin conformation that juxtaposes the viral and cellular membranes to facilitate membrane fusion and enable subsequent viral entry. The Hendra and Nipah virus fusion core proteins were crystallized and their structures determined to 2.2 A resolution. The Nipah and Hendra fusion core structures are six-helix bundles with three HR2 helices packed against the hydrophobic grooves on the surface of a central coiled coil formed by three parallel HR1 helices in an oblique antiparallel manner. Because of the high level of conservation in core regions, it is proposed that the Nipah and Hendra virus fusion cores can provide a model for membrane fusion in all paramyxoviruses. The relatively deep grooves on the surface of the central coiled coil represent a good target site for drug discovery strategies aimed at inhibiting viral entry by blocking hairpin formation.
  13. Guo K, Zhang X, Bai S, Minhat HS, Nazan AINM, Feng J, et al.
    PLoS One, 2021;16(7):e0253891.
    PMID: 34297731 DOI: 10.1371/journal.pone.0253891
    Following the 2019 coronavirus disease (COVID-19) outbreak in China, undergraduate students may experience psychological changes. During emergency circumstances, social support is an important factor influencing the mental health condition among undergraduate students in Shaanxi province. This study aims to find the factors associated with mental health symptoms of depression, anxiety, and stress among undergraduate students in Shaanxi province during the COVID-19 pandemic in China. A cross-sectional study was conducted from Feb 23 to Mar 7, 2020. A total of 1278 undergraduate students from the universities located in Shaanxi province participated in this study. The mental health symptoms were measured by 12-item Perceived Social Support Scale (PSSS) and Depression Anxiety Stress Scale (DASS-21) instruments. This survey showed that females receive more social support compared to males (t = -5.046, P<0.001); males have higher-level depression symptoms (t = 5.624, P<0.001); males have higher-level anxiety symptoms (t = 6.332, P<0.001), males have higher-level stress symptoms (t = 5.58, P<0.001). This study also found participants who have low social support was negatively correlated with mental health symptoms. In Conclusion, Males and low social support were associated with having the higher level of depression, anxiety, and stress symptoms among undergraduate students in Shaanxi province during the COVID-19 pandemic in China. Therefore, it is suggested that people should supply more social support for undergraduate students in Shaanxi province during COVID-19 pandemic.
  14. Tay K, Kamarul T, Lok WY, Mansor M, Li X, Wong J, et al.
    Malays Orthop J, 2020 Jul;14(2).
    PMID: 32313613 DOI: 10.5704/MOJ.2007.001
    With the increasing number of COVID-19 cases and related deaths worldwide, we decided to share the development of this condition in Singapore and Malaysia. First few cases were diagnosed in the two countries at the end of January 2020, and the numbers have surged to thousands by end of March 2020. We will focus on strategies adopted by the government and also the Orthopaedic community of the two countries up till the beginning of April 2020. We hope that by sharing of relevant information and knowledge on how we are managing the COVID-19 condition, we can help other communities, and health care workers to more effectively overcome this pandemic.
  15. Tang W, Liu H, Li X, Ooi TC, Rajab NF, Cao H, et al.
    Aging (Albany NY), 2022 Nov 14;14(21):8688-8699.
    PMID: 36375474 DOI: 10.18632/aging.204380
    BACKGROUND: A complex of Zn and carnosine, called Zinc-L-carnosine (ZnC), enjoys a wide application as part of a Zn supplement therapeutic method as well as in treating peptic ulcers. However, researches fail to confirm the biological functions possessed by ZnC as well as tumor immune microenvironment in colorectal cancer (CRC).

    METHODS: Cell counting kit 8(CCK8), 5-ethynyl-2'-deoxyuridine (EdU), transwell and wound healing assays were conducted to study the influence of ZnC in the proliferating, invading and migrating processes of CRC cell lines (HCT116, LOVO) in vitro. The antitumor activity ZnC as well as its effects on tumor immune microenvironment were then assessed using CRC subcutaneous tumors in the C57BL/6 mouse model.

    RESULTS: According to CCK8, EdU, transwell and wound healing assays, ZnC inhibited CRC cell lines in terms of proliferation, invasion and migration. ZnC could inhibit miR-570 for up-regulating PD-L1 expression. In vivo experiments showed that gavage (100 mg/kg, once every day) of ZnC inhibited the tumor growth of CRC, and the combination of ZnC and anti-PD1 therapy significantly improved the efficacy exhibited by anti-PD1 in treating CRC. In addition, mass cytometry results showed that immunosuppressive cells including regulatory T cells (tregs), bone marrow-derived suppressor cells (MDSC), and M2 macrophages decreased whereas CD8+ T cells elevated after adding ZnC.

    CONCLUSIONS: The present study reveals that ZnC slows the progression of CRC by inhibiting CRC cells in terms of proliferation, invasion and migration, meanwhile up-regulating PD-L1 expression via inhibiting miR-570. The ZnC-anti-PD1 co-treatment assists in synergically increasing anti-tumor efficacy in CRC therapy.

  16. Tang W, Liu H, Li X, Ooi TC, Rajab NF, Cao H, et al.
    J Oncol, 2023;2023:2611105.
    PMID: 36908705 DOI: 10.1155/2023/2611105
    BACKGROUND: Approximately 10% of cancer patients worldwide have colorectal cancer (CRC), a prevalent gastrointestinal malignancy with substantial mortality and morbidity. The purpose of this work was to investigate the APOC1 gene's expression patterns in the CRC tumor microenvironment and, using the findings from bioinformatics, to assess the biological function of APOC1 in the development of CRC.

    METHODS: The TCGA portal was employed in this investigation to find APOC1 expression in CRC. Its correlation with other genes and clinicopathological data was examined using the UALCAN database. To validate APOC1's cellular location, the Human Protein was employed. In order to forecast the relationship between APOC1 expression and prognosis in CRC patients, the Kaplan-Meier plotter database was used. TISIDB was also employed to evaluate the connection between immune responses and APOC1 expression in CRC. The interactions of APOC1 with other proteins were predicted using STRING. In order to understand the factors that contribute to liver metastasis from CRC, single-cell RNA sequencing (scRNA-seq) was done on one patient who had the disease. This procedure included sampling preoperative blood and the main colorectal cancer tissues, surrounding colorectal cancer normal tissues, liver metastatic cancer tissues, and normal liver tissues. Finally, an in vitro knockdown method was used to assess how APOC1 expression in tumor-associated macrophages (TAMs) affected CRC cancer cell growth and migration.

    RESULTS: When compared to paracancerous tissues, APOC1 expression was considerably higher in CRC tissues. The clinicopathological stage and the prognosis of CRC patients had a positive correlation with APOC1 upregulation and a negative correlation, respectively. APOC1 proteins are mostly found in cell cytosols where they may interact with APOE, RAB42, and TREM2. APOC1 was also discovered to have a substantial relationship with immunoinhibitors (CD274, IDO1, and IL10) and immunostimulators (PVR, CD86, and ICOS). According to the results of scRNA-seq, we found that TAMs of CRC tissues had considerably more APOC1 than other cell groups. The proliferation and migration of CRC cells were impeded in vitro by APOC1 knockdown in TAMs.

    CONCLUSION: Based on scRNA-seq research, the current study shows that APOC1 was overexpressed in TAMs from CRC tissues. By inhibiting APOC1 in TAMs, CRC progression was reduced in vitro, offering a new tactic and giving CRC patients fresh hope.

  17. Xiao K, Zhai J, Feng Y, Zhou N, Zhang X, Zou JJ, et al.
    Nature, 2020 07;583(7815):286-289.
    PMID: 32380510 DOI: 10.1038/s41586-020-2313-x
    The current outbreak of coronavirus disease-2019 (COVID-19) poses unprecedented challenges to global health1. The new coronavirus responsible for this outbreak-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-shares high sequence identity to SARS-CoV and a bat coronavirus, RaTG132. Although bats may be the reservoir host for a variety of coronaviruses3,4, it remains unknown whether SARS-CoV-2 has additional host species. Here we show that a coronavirus, which we name pangolin-CoV, isolated from a Malayan pangolin has 100%, 98.6%, 97.8% and 90.7% amino acid identity with SARS-CoV-2 in the E, M, N and S proteins, respectively. In particular, the receptor-binding domain of the S protein of pangolin-CoV is almost identical to that of SARS-CoV-2, with one difference in a noncritical amino acid. Our comparative genomic analysis suggests that SARS-CoV-2 may have originated in the recombination of a virus similar to pangolin-CoV with one similar to RaTG13. Pangolin-CoV was detected in 17 out of the 25 Malayan pangolins that we analysed. Infected pangolins showed clinical signs and histological changes, and circulating antibodies against pangolin-CoV reacted with the S protein of SARS-CoV-2. The isolation of a coronavirus from pangolins that is closely related to SARS-CoV-2 suggests that these animals have the potential to act as an intermediate host of SARS-CoV-2. This newly identified coronavirus from pangolins-the most-trafficked mammal in the illegal wildlife trade-could represent a future threat to public health if wildlife trade is not effectively controlled.
  18. Yang Y, Li J, Yang S, Li X, Fang L, Zhong C, et al.
    BMC Evol. Biol., 2017 01 18;17(1):22.
    PMID: 28100168 DOI: 10.1186/s12862-016-0849-z
    BACKGROUND: A large-scale systematical investigation of the influence of Pleistocene climate oscillation on mangrove population dynamics could enrich our knowledge about the evolutionary history during times of historical climate change, which in turn may provide important information for their conservation.

    RESULTS: In this study, phylogeography of a mangrove tree Sonneratia alba was studied by sequencing three chloroplast fragments and seven nuclear genes. A low level of genetic diversity at the population level was detected across its range, especially at the range margins, which was mainly attributed to the steep sea-level drop and associated climate fluctuations during the Pleistocene glacial periods. Extremely small effective population size (Ne) was inferred in populations from both eastern and western Malay Peninsula (44 and 396, respectively), mirroring the fragility of mangrove plants and their paucity of robustness against future climate perturbations and human activity. Two major genetic lineages of high divergence were identified in the two mangrove biodiversity centres: the Indo-Malesia and Australasia regions. The estimated splitting time between these two lineages was 3.153 million year ago (MYA), suggesting a role for pre-Pleistocene events in shaping the major diversity patterns of mangrove species. Within the Indo-Malesia region, a subdivision was implicated between the South China Sea (SCS) and the remaining area with a divergence time of 1.874 MYA, corresponding to glacial vicariance when the emerged Sunda Shelf halted genetic exchange between the western and eastern coasts of the Malay Peninsula during Pleistocene sea-level drops. Notably, genetic admixture was observed in populations at the boundary regions, especially in the two populations near the Malacca Strait, indicating secondary contact between divergent lineages during interglacial periods. These interregional genetic exchanges provided ample opportunity for the re-use of standing genetic variation, which could facilitate mangrove establishment and adaptation in new habitats, especially in the context of global climate changes.

    CONCLUSION: Phylogeogrpahic analysis in this study reveal that Pleistocene sea-level fluctuations had profound influence on population differentiation of the mangrove tree S. alba. Our study highlights the fragility of mangrove plants and offers a guide for the conservation of coastal mangrove communities experiencing ongoing changes in sea-level.

  19. He Z, Li X, Yang M, Wang X, Zhong C, Duke NC, et al.
    Natl Sci Rev, 2019 Mar;6(2):275-288.
    PMID: 31258952 DOI: 10.1093/nsr/nwy078
    Allopatric speciation requiring an unbroken period of geographical isolation has been the standard model of neo-Darwinism. While doubts have been repeatedly raised, strict allopatry without any gene flow remains a plausible mechanism in most cases. To rigorously reject strict allopatry, genomic sequences superimposed on the geological records of a well-delineated geographical barrier are necessary. The Strait of Malacca, narrowly connecting the Pacific and Indian Ocean coasts, serves at different times either as a geographical barrier or a conduit of gene flow for coastal/marine species. We surveyed 1700 plants from 29 populations of 5 common mangrove species by large-scale DNA sequencing and added several whole-genome assemblies. Speciation between the two oceans is driven by cycles of isolation and gene flow due to the fluctuations in sea level leading to the opening/closing of the Strait to ocean currents. Because the time required for speciation in mangroves is longer than the isolation phases, speciation in these mangroves has proceeded through many cycles of mixing-isolation-mixing, or MIM, cycles. the MIM mechanism, by relaxing the condition of no gene flow, can promote speciation in many more geographical features than strict allopatry can. Finally, the MIM mechanism of speciation is also efficient, potentially yielding m n (m > 1) species ather n cycles.

    SIGNIFICANCE STATEMENT: Mechanisms of species formation have always been a conundrum. Speciation between populations that are fully geographically isolated, or allopatric speciation, has been the standard solution in the last 50 years. Complete geographical isolation with no possibility of gene flow, however, is often untenable and is inefficient in generating the enormous biodiversity. By studying mangroves on the Indo-Malayan coasts, a global hotspot of coastal biodiversity, we were able to combine genomic data with geographical records on the Indo-Pacific Barrier that separates Pacific and Indian Ocean coasts. We discovered a novel mechanism of speciation that we call mixingisolation-mixing (MIM) cycles. By permitting intermittent gene flow during speciation,MIMcycles can potentially generate species at an exponential rate, thus combining speciation and biodiversity in a unified framework.

  20. Li X, Wang X, Song T, Lu W, Chen Z, Shi X
    J Anal Methods Chem, 2015;2015:675827.
    PMID: 26491602 DOI: 10.1155/2015/675827
    DNA strand displacement technique is widely used in DNA programming, DNA biosensors, and gene analysis. In DNA strand displacement, leaky reactions can cause DNA signals decay and detecting DNA signals fails. The mostly used method to avoid leakage is cleaning up after upstream leaky reactions, and it remains a challenge to develop reliable DNA strand displacement technique with low leakage. In this work, we address the challenge by experimentally evaluating the basic factors, including reaction time, ratio of reactants, and ion concentration to the leakage in DNA strand displacement. Specifically, fluorescent probes and a hairpin structure reporting DNA strand are designed to detect the output of DNA strand displacement, and thus can evaluate the leakage of DNA strand displacement reactions with different reaction time, ratios of reactants, and ion concentrations. From the obtained data, mathematical models for evaluating leakage are achieved by curve derivation. As a result, it is obtained that long time incubation, high concentration of fuel strand, and inappropriate amount of ion concentration can weaken leaky reactions. This contributes to a method to set proper reaction conditions to reduce leakage in DNA strand displacement.
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