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Unleashing Breast Cancer Progression: miR-455-5p's Targeting of SOCS3 Drives Proliferation, Migration, and Invasion

Li X, Peng B, Li J, Tian M, He L

Protein Pept Lett, 2023;30(12):992-1000.
PMID: 38013437 DOI: 10.2174/0109298665245603231106050224

OBJECTIVES: We aim to investigate the regulatory mechanisms of miR-455-5p/SOCS3 pathway that underlie the proliferation, migration, and invasion of triple-negative breast cancer (TNBC) cells.
METHODS: Reverse transcription-quantitative PCR (RT-qPCR) was used to detect miR-455-5p expression in breast cancer tissues and cell lines. CCK8 and Transwell assays were conducted to assess the effects of miR-455-5p on breast cancer line proliferation, migration, and invasion. SOCS3 expression level in breast cancer tissues and cell lines was determined by qPCR and western blotting. The targeting relationship between miR-455-5p and SOCS3 was determined by dual luciferase reporter gene assay in different breast cancer cell lines. Finally, the upstream and downstream regulatory association between miR-455-5p and SOCS3 was confirmed in breast cancer cells by CCK8, western blot, and Transwell assays.
RESULTS: MiR-455-5p expression was up-regulated in breast cancer tissues; miR-455-5p regulates TNBC proliferation, migration, and invasion of TNBC. SOCS3 was the direct target of miR-455-5p and was down-regulated in breast cancer. Interference with SOCS3 reversed the inhibitory effect of the miR-455-5p inhibitor on breast cancer cells' malignant potential.
CONCLUSION: MiR-455-5p promotes breast cancer progression by targeting the SOCS3 pathway and may be a potential therapeutic target for breast cancer.
Seasonal impact of constructed wetlands on nitrogen and phosphorus in sediments of flood control lakes with pollution assessment

Li X, Liu X, Huang Y, Zhang Y, Li J

J Environ Qual, 2024 Apr 10.
PMID: 38595076 DOI: 10.1002/jeq2.20561

The primary drivers of eutrophication in lakes following the reduction of external nutrient inputs are the release of N and P from sediments. Constructed wetlands play a pivotal role in ameliorating N, P, and other biogenic element levels. However, the presence of large vegetation in these wetlands also substantially contributes to nutrient accumulation in sediments, a phenomenon influenced by seasonal variations. In this study, a typical constructed wetland was selected as the research site. The research aimed to analyze the forms of N and P in sediments during both summer and winter. Simultaneously, a comprehensive pollution assessment and analysis were conducted within the study area. The findings indicate that elevated summer temperatures, together with the presence of wetland vegetation, promote the release of N through the nitrification process. Additionally, seasonal variations exert a significant impact on the distribution of P storage. Furthermore, the role of constructed wetlands in the absorption and release of N and P is primarily controlled by the influence of organic matter on nitrate-nitrogen, nitrite-nitrogen, and available phosphorus, and is also subject to seasonal fluctuations. In summary, under the comprehensive influence of constructed wetlands, vegetation types, and seasons, sediments within the lake generally exhibit a state of mild or moderate pollution. Therefore, targeted measures should be adopted to optimally adjust vegetation types, and human intervention is necessary, involving timely sediment harvesting during the summer to reduce N and P loads, and enhancing sediment adsorption and retention capacity for N and P during the winter.
Fulltext Geographic wormhole detection in wireless sensor networks

Sookhak M, Akhundzada A, Sookhak A, Eslaminejad M, Gani A, Khurram Khan M, et al.

PLoS One, 2015;10(1):e0115324.
PMID: 25602616 DOI: 10.1371/journal.pone.0115324

Wireless sensor networks (WSNs) are ubiquitous and pervasive, and therefore; highly susceptible to a number of security attacks. Denial of Service (DoS) attack is considered the most dominant and a major threat to WSNs. Moreover, the wormhole attack represents one of the potential forms of the Denial of Service (DoS) attack. Besides, crafting the wormhole attack is comparatively simple; though, its detection is nontrivial. On the contrary, the extant wormhole defense methods need both specialized hardware and strong assumptions to defend against static and dynamic wormhole attack. The ensuing paper introduces a novel scheme to detect wormhole attacks in a geographic routing protocol (DWGRP). The main contribution of this paper is to detect malicious nodes and select the best and the most reliable neighbors based on pairwise key pre-distribution technique and the beacon packet. Moreover, this novel technique is not subject to any specific assumption, requirement, or specialized hardware, such as a precise synchronized clock. The proposed detection method is validated by comparisons with several related techniques in the literature, such as Received Signal Strength (RSS), Authentication of Nodes Scheme (ANS), Wormhole Detection uses Hound Packet (WHOP), and Wormhole Detection with Neighborhood Information (WDI) using the NS-2 simulator. The analysis of the simulations shows promising results with low False Detection Rate (FDR) in the geographic routing protocols.
Prevalence, racial variations, and risk factors of age-related macular degeneration in Singaporean Chinese, Indians, and Malays

Cheung CM, Li X, Cheng CY, Zheng Y, Mitchell P, Wang JJ, et al.

Ophthalmology, 2014 Aug;121(8):1598-603.
PMID: 24661862 DOI: 10.1016/j.ophtha.2014.02.004

To describe the prevalence and risk factors for age-related macular degeneration (AMD) in a multiethnic Asian cohort of Chinese, Malay, and Indian persons.
Crystal structures of Nipah and Hendra virus fusion core proteins

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.
Fractionation of oil palm empty fruit bunch by bisulfite pretreatment for the production of bioethanol and high value products

Tan L, Wang M, Li X, Li H, Zhao J, Qu Y, et al.

Bioresour Technol, 2016 Jan;200:572-8.
PMID: 26539970 DOI: 10.1016/j.biortech.2015.10.079

In this work, fractionation of empty fruit bunch (EFB) by bisulfite pretreatment was studied for the production of bioethanol and high value products to achieve biorefinery of EFB. EFB was fractionated to solid and liquor components by bisulfite process. The solid components were used for bioethanol production by quasi-simultaneous saccharification and fermentation. The liquor components were then converted to furfural by hydrolysis with sulfuric acid. Preliminary results showed that the concentration of furfural was highest at 18.8g/L with 0.75% sulfuric acid and reaction time of 25min. The conversion of xylose to furfural was 82.5%. Furthermore, we attempted to fractionate the liquor into hemicellulose sugars and lignin by different methods for producing potential chemicals, such as xylose, xylooligosaccharide, and lignosulfonate. Our research showed that the combination of bisulfite pretreatment and resin separation could effectively fractionate EFB components to produce bioethanol and other high value chemicals.
Fulltext [Analysis of heavy-metal-mediated disease and development of a novel remediation system based on fieldwork and experimental research]

Yajima I, Zou C, Li X, Nakano C, Omata Y, Kumasaka MY

Nihon Eiseigaku Zasshi, 2015;70(2):105-9.
PMID: 25994340 DOI: 10.1265/jjh.70.105

Heavy-metal pollution occurs in various environments, including water, air and soil, and has serious effects on human health. Since heavy-metal pollution in drinking water causes various diseases including skin cancer, it has become a global problem worldwide. However, there is limited information on the mechanism of development of heavy-metal-mediated disease. We performed both fieldwork and experimental studies to elucidate the levels of heavy-metal pollution and mechanisms of development of heavy-metal-related disease and to develop a novel remediation system. Our fieldwork in Bangladesh, Vietnam and Malaysia demonstrated that drinking well water in these countries was polluted with high concentrations of several heavy metals including arsenic, barium, iron and manganese. Our experimental studies based on the data from our fieldwork demonstrated that these heavy metals caused skin cancer and hearing loss. Further experimental studies resulted in the development of a novel remediation system with which toxic heavy metals were absorbed from polluted drinking water. Implementation of both fieldwork and experimental studies is important for prediction, prevention and therapy of heavy-metal-mediated diseases.
Bisulfite pretreatment changes the structure and properties of oil palm empty fruit bunch to improve enzymatic hydrolysis and bioethanol production

Tan L, Sun W, Li X, Zhao J, Qu Y, Choo YM, et al.

Biotechnol J, 2015 Jun;10(6):915-25.
PMID: 25866127 DOI: 10.1002/biot.201400733

Bisulfite pretreatment is a proven effective method for improving the enzymatic hydrolysis of empty fruit bunch (EFB) from oil palm for bioethanol production. In this study, we set out to determine the changes that occur in the structure and properties of EFB materials and fractions of hemicellulose and lignin during the bisulfite pretreatment process. The results showed that the crystallinity of cellulose in EFB increased after bisulfite pretreatment, whereas the EFB surface was damaged to various degrees. The orderly structure of EFB, which was maintained by hydrogen bonds, was destroyed by bisulfite pretreatment. Bisulfite pretreatment also hydrolyzed the glycosidic bonds of the xylan backbone of hemicellulose, thereby decreasing the molecular weight and shortening the xylan chains. The lignin fractions obtained from EFB and pretreated EFB were typically G-S lignin, and with low content of H units. Meanwhile, de-etherification occurred at the β-O-4 linkage, which was accompanied by polymerization and demethoxylation as a result of bisulfite pretreatment. The adsorption ability of cellulase differed for the various lignin fractions, and the water-soluble lignin fractions had higher adsorption capacity on cellulase than the milled wood lignin. In general, the changes in the structure and properties of EFB provided insight into the benefits of bisulfite pretreatment.
Fulltext Organotypic slice culture based on in ovo electroporation for chicken embryonic central nervous system

Yang C, Li X, Li S, Chai X, Guan L, Qiao L, et al.

J Cell Mol Med, 2019 03;23(3):1813-1826.
PMID: 30565384 DOI: 10.1111/jcmm.14080

Organotypic slice culture is a living cell research technique which blends features of both in vivo and in vitro techniques. While organotypic brain slice culture techniques have been well established in rodents, there are few reports on the study of organotypic slice culture, especially of the central nervous system (CNS), in chicken embryos. We established a combined in ovo electroporation and organotypic slice culture method to study exogenous genes functions in the CNS during chicken embryo development. We performed in ovo electroporation in the spinal cord or optic tectum prior to slice culture. When embryonic development reached a specific stage, green fluorescent protein (GFP)-positive embryos were selected and fluorescent expression sites were cut under stereo fluorescence microscopy. Selected tissues were embedded in 4% agar. Tissues were sectioned on a vibratory microtome and 300 μm thick sections were mounted on a membrane of millicell cell culture insert. The insert was placed in a 30-mm culture dish and 1 ml of slice culture media was added. We show that during serum-free medium culture, the slice loses its original structure and propensity to be strictly regulated, which are the characteristics of the CNS. However, after adding serum, the histological structure of cultured-tissue slices was able to be well maintained and neuronal axons were significantly longer than that those of serum-free medium cultured-tissue slices. As the structure of a complete single neuron can be observed from a slice culture, this is a suitable way of studying single neuronal dynamics. As such, we present an effective method to study axon formation and migration of single neurons in vitro.
Fulltext Wind-driven development and transport of Gymnodinium catenatum blooms along the coast of Fujian, China

Zhang C, Lim PT, Li X, Gu H, Li X, Anderson DM

Reg Stud Mar Sci, 2020 Sep;39.
PMID: 33241099 DOI: 10.1016/j.rsma.2020.101397

Gymnodinium catenatum is a cosmopolitan, bloom-forming dinoflagellate known to produce a suite of potent paralytic shellfish poisoning (PSP) toxins. Here, we revisit two major blooms of G. catenatum along the Fujianese Coast, China, in 2017 and 2018. The impact area of the 2017 bloom was larger than that of the 2018 event. Field sampling and remote satellite sensing revealed that alongshore transport driven by the southwest wind, as well as physical accumulation driven by the northeast wind, played important roles in the development and distribution of the two bloom events. The relationship between wind-induced hydrodynamic conditions and the unprecedented HAB events established in this study adds greatly to our understanding of algal bloom dynamics along the Fujianese coast. These results improve our ability to detect, track, and forecast G. catenatum blooms, thereby potentially minimizing the negative impacts of future HAB events.
Fulltext Different Concentrations of Doxycycline in Swine Manure Affect the Microbiome and Degradation of Doxycycline Residue in Soil

Yan Q, Li X, Ma B, Zou Y, Wang Y, Liao X, et al.

Front Microbiol, 2018;9:3129.
PMID: 30619199 DOI: 10.3389/fmicb.2018.03129

Antibiotic residues that enter the soil through swine manure could disturb the number, community structure and functions of microbiota which could also degrade antibiotics in soil. Five different concentrations of doxycycline (DOX) incorporated into swine manure were added to soil to explore the effects of DOX on microbiota in soil and degradation itself. The results showed that the soil microbiome evolved an adaptation to the soil containing DOX by generating resistance genes. Moreover, some of the organisms within the soil microbiome played crucial roles in the degradation of DOX. The average degradation half-life of DOX in non-sterile groups was 13.85 ± 0.45 days, which was significantly shorter than the 29.26 ± 0.98 days in the group with sterilized soil (P < 0.01), indicating that the soil microbiome promoted DOX degradation. DOX addition affected the number of tetracycline resistance genes, depending on the type of gene and the DOX concentration. Among these genes, tetA, tetM, tetW, and tetX had significantly higher copy numbers when the concentration of DOX was higher. In contrast, a lower concentration of DOX had an inhibitory effect on tetG. At the same time, the microbial compositions were affected by the initial concentration of DOX and the different experimental periods. The soil chemical indicators also affected the microbial diversity changes, mainly because some microorganisms could survive in adversity and become dominant bacterial groups, such as the genera Vagococcus and Enterococcus (which were associated with electrical conductivity) and Caldicoprobacter spp. (which were positively correlated with pH). Our study mainly revealed soil microbiota and DOX degradation answered differently under variable concentrations of DOX mixed with swine manure in soil.
An overview of signaling pathways regulating YAP/TAZ activity

Heng BC, Zhang X, Aubel D, Bai Y, Li X, Wei Y, et al.

Cell Mol Life Sci, 2021 Jan;78(2):497-512.
PMID: 32748155 DOI: 10.1007/s00018-020-03579-8

YAP and TAZ are ubiquitously expressed homologous proteins originally identified as penultimate effectors of the Hippo signaling pathway, which plays a key role in maintaining mammalian tissue/organ size. Presently, it is known that YAP/TAZ also interact with various non-Hippo signaling pathways, and have diverse roles in multiple biological processes, including cell proliferation, tissue regeneration, cell lineage fate determination, tumorigenesis, and mechanosensing. In this review, we first examine the various microenvironmental cues and signaling pathways that regulate YAP/TAZ activation, through the Hippo and non-Hippo signaling pathways. This is followed by a brief summary of the interactions of YAP/TAZ with TEAD1-4 and a diverse array of other non-TEAD transcription factors. Finally, we offer a critical perspective on how increasing knowledge of the regulatory mechanisms of YAP/TAZ signaling might open the door to novel therapeutic applications in the interrelated fields of biomaterials, tissue engineering, regenerative medicine and synthetic biology.
Superior photoelectrocatalytic performance of ternary structural BiVO4/GQD/g-C3N4 heterojunction

Samsudin MFR, Ullah H, Tahir AA, Li X, Ng YH, Sufian S

J Colloid Interface Sci, 2021 Mar 15;586:785-796.
PMID: 33198982 DOI: 10.1016/j.jcis.2020.11.003

Herein, we performed an encyclopedic analysis on the photoelectrocatalytic hydrogen production of BiVO4/g-C3N4 decorated with reduced graphene oxide (RGO) or graphene quantum dots (GQDs). The differences between RGO and GQDs as an electron mediator was revealed for the first time in the perspective of theoretical DFT analysis and experimental validation. It was found that the incorporation of GQDs as an electron mediator promotes better photoelectrocatalytic hydrogen performance in comparison to the RGO. The addition of GQD can significantly improve the activity by 25.2 and 75.7% in comparison to the BiVO4/RGO/g-C3N4 and binary composite samples, respectively. Correspondingly, the BiVO4/GQD/g-C3N4 attained the highest photocurrent density of 19.2 mA/cm2 with an ABPE of 0.57% without the presence of any sacrificial reagents. This enhancement is stemming from the low photocharge carrier transfer resistance which was further verified via DFT study. The DFT analysis revealed that the BiVO4/GQD/g-C3N4 sample shared their electronic cloud density through orbital hybridization while the BiVO4/RGO/g-C3N4 sample show less mutual sharing. Additionally, the charge redistribution of the GQDs-composite at the heterostructure interface articulates a more stable and stronger heterojunction than the RGO-composite. Notably, this study provides new insights on the effect of different carbonaceous materials (RGO and GQDs) which are often used as an electron mediator to enhance photocatalytic activity.
Association between serum vitamin D levels and venous thromboembolism (VTE): A systematic review and meta-analysis of observational studies

Wan J, Yuan J, Li X, Bao Y, Hou Y, Li Z, et al.

Complement Ther Med, 2020 Nov;54:102579.
PMID: 33183675 DOI: 10.1016/j.ctim.2020.102579

OBJECTIVE: Although many studies have attempted to unravel the relationship between vitamin D deficiency and the incidence of VTE, the results remained inconsistent. To address this discrepancy, we performed a systematic review and meta-analysis to precisely disentangle the relationship between serum vitamin D levels and VTE risk.
METHODS: The Web of Science, Scopus, PubMed/Medline, Embase, and Google Scholar databases were searched for all available observational studies that reported the risk of venous thromboembolism (VTE) based on serum vitamin D levels categories. The search was performed up to March 2020.
RESULTS: Seven studies were included. The overall analysis showed a significantly increased risk of VTE in subjects with low levels of serum vitamin D compared with those with normal vitamin D levels (RR = 1.34; 95% CI: 1.07-1.69; P = 0.011). In a sensitivity analysis, we did not observe a significant effect of any individual study on the combined effect sizes. Nevertheless, significant heterogeneity was present among the studies (Cochrane Q test, p = 0.018, I2 = 61%). In the stratified analysis, low vitamin D levels were positively associated with an increased risk of VTE in prospective population-based studies (RR = 1.31; 95% CI: 1.06-1.61; P = 0.010) and in subjects below 60 years old (RR = 1.28; 95% CI: 1.07-1.54; P = 0.060).
CONCLUSION: our systematic review and meta-analysis showed that a low serum vitamin D level was indeed associated with an increased risk of VTE.
Corrigendum to "Superior photoelectrocatalytic performance of ternary structural BiVO4/GQD/g-C3N4 heterojunction" [J. Col. Interf. Sci. 586 (2021) 785-796]

Fakhrul Ridhwan Samsudin M, Ullah H, Tahir AA, Li X, Hau Ng Y, Sufian S

J Colloid Interface Sci, 2021 Nov 15;602:900.
PMID: 34088501 DOI: 10.1016/j.jcis.2021.04.096
Associations between TNFSF4 gene polymorphisms (rs2205960 G > A, rs704840 T > G and rs844648 G > A) and susceptibility to autoimmune diseases in Asians: a meta-analysis

Yang Y, Li X, Li B, Mu L, Wang J, Cheng Y, et al.

Immunol Invest, 2021 Feb;50(2-3):184-200.
PMID: 32208776 DOI: 10.1080/08820139.2020.1718693

BACKGROUND: Tumor necrosis factor superfamily member 4 (TNFSF4) has significant role in modulating autoimmune diseases (ADs) and single nucleotide polymorphism (SNP) is also related with the susceptibility to some diseases. So a meta-analysis aimed at systematically assessing the associations between TNFSF4 polymorphisms (rs2205960 G > A, rs704840 T > G and rs844648 G > A) and ADs risk was performed in Asians.
METHODS: Total 14 eligible articles published before March 2019 involving 35 studies, of which 21 studies (16,109 cases and 26,378 controls) for rs2205960 G > A, 8 studies (2,424 cases and 3,692 controls) for rs704840 T > G, and 6 studies (3,839 cases and 5,867 controls) for rs844648 G > A were included. Effects of the three respective polymorphisms on the susceptibility to ADs were estimated by pooling the odds ratios (ORs) with their corresponding 95% confidence interval (95% CI) in allelic, dominant, recessive, heterozygous and homozygous models.
RESULTS: The overall analysis revealed that all the rs2205960 G > A, rs704840 T > G and rs844648 G > A polymorphisms could increase the risk of ADs in allelic, dominant, recessive, heterozygous and homozygous models. Furthermore, subgroup analysis showed that both rs2205960 G > A and rs704840 T > G were significantly associated with the susceptibility to systemic lupus erythematosus (SLE). What's more, statistically significant association between rs2205960 G > A polymorphism and primary Sjögren's syndrome (pSS) susceptibility was also observed in allelic, dominant and heterozygous models.
CONCLUSIONS: This current meta-analysis suggested that all of the three TNFSF4 polymorphisms may be associated with ADs susceptibility in Asians.
Fulltext High Vitamin D Levels May Downregulate Inflammation in Patients with Behçet's Disease

Adeeb F, Khan MU, Li X, Stack AG, Devlin J, Fraser AD

Int J Inflam, 2017;2017:8608716.
PMID: 28660088 DOI: 10.1155/2017/8608716

Vitamin D plays a significant role in the immune system modulation and may confer a protective role in autoimmune diseases. We conducted a case-control study to compare 25(OH)D levels in patients with BD who were managed at a regional rheumatology programme in the midwest region of Ireland compared to matched controls. Healthy controls were selected from the Irish health system and matched in 1 : 5 ratio for age, sex, and the month of the year. 25(OH)D levels <20 nmol/L were classified as deficient while levels between 20 and 40 nmol/L were classified as insufficient. Differences between groups were assessed using Mann-Whitney test and associations between cases and controls were expressed as odds ratios and 95% confidence intervals. Nineteen patients with BD were compared with 95 controls matched by age, sex, and month of blood draw. 25(OH)D levels were significantly higher in patients in BD than in matched controls (median values: 45 nmol/L versus 22 nmol/L, p < 0.005) and tended to be lower in patients with active disease than in those without (median values: 35 nmol/L (IQR: 22.75-47.25 nm/L) versus 50 nmol/L (IQR: 35-67 nmol/L), p = 0.11). Compared to controls, patients with BD were significantly less likely to have 25(OH)D deficiency or insufficiency (OR: 0.09, 95% CI: 0.03-0.28, p < 0.001). Our findings suggest a possible role for 25(OH)D in modifying the inflammatory response in BD and uncover a potential opportunity to assess whether correction of Vit D deficiency confers protective benefits.
Fulltext Effects of Pleistocene sea-level fluctuations on mangrove population dynamics: a lesson from Sonneratia alba

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.
De novo assembly of genome and development of polymorphic microsatellite loci in the blue swimming crab (Portunus pelagicus) using RAD approach

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.
Fulltext Effect of sonic hedgehog on motor neuron positioning in the spinal cord during chicken embryonic development

Yang C, Li S, Li X, Li H, Li Y, Zhang C, et al.

J Cell Mol Med, 2019 05;23(5):3549-3562.
PMID: 30834718 DOI: 10.1111/jcmm.14254

Sonic hedgehog (SHH) is a vertebrate homologue of the secreted Drosophila protein hedgehog and is expressed by the notochord and floor plate in the developing spinal cord. Sonic hedgehog provides signals relevant for positional information, cell proliferation and possibly cell survival, depending on the time and location of expression. Although the role of SHH in providing positional information in the neural tube has been experimentally proven, the underlying mechanism remains unclear. In this study, in ovo electroporation was employed in the chicken spinal cord during chicken embryo development. Electroporation was conducted at stage 17 (E2.5), after electroporation the embryos were continued incubating to stage 28 (E6) for sampling, tissue fixation with 4% paraformaldehyde and frozen sectioning. Sonic hedgehog and related protein expressions were detected by in situ hybridization and fluorescence immunohistochemistry and the results were analysed after microphotography. Our results indicate that the ectopic expression of SHH leads to ventralization in the spinal cord during chicken embryonic development by inducing abnormalities in the structure of the motor column and motor neuron integration. In addition, ectopic SHH expression inhibits the expression of dorsal transcription factors and commissural axon projections. The correct location of SHH expression is vital to the formation of the motor column. Ectopic expression of SHH in the spinal cord not only affects the positioning of motor neurons, but also induces abnormalities in the structure of the motor column. It leads to ventralization in the spinal cord, resulting in the formation of more ventral neurons forming during neuronal formation.

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