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Zhao P, Wang L, Zhao X, Chen G, Ma XF. A comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in Braya humilis. PLoS One 2017; 12:e0183778. [PMID: 28859098 PMCID: PMC5578489 DOI: 10.1371/journal.pone.0183778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 08/10/2017] [Indexed: 11/25/2022] Open
Abstract
Braya humilis is a member of the Euclidieae tribe within the family Brassicaceae. This species exhibits a broad range of adaptations to different climatic zones and latitudes as it has a distribution that ranges from northern Asia to the arctic-alpine regions of northern North America. In China, B. humilis is mainly found on the Qinghai-Tibetan Plateau (QTP) and in adjacent arid regions. In this study, we sequenced a sample from an arid region adjacent to the QTP using the Illumina platform generating a total of 46,485 highly accurate unigenes, of which 78.41% were annotated by BLASTing versus public protein databases. The B. humilis transcriptome is characterized by a high level of sequence conservation compared with its close relative, Arabidopsis thaliana. We also used reciprocal blast to identify shared orthologous genes between B. humilis and four other sequenced Brassicaceae species (i.e. A. thaliana, A. lyrata, Capsella rubella, and Thellungiella parvula). To enable precise characterization of orthologous genes, the early-diverging basal angiosperm Amborella trichopoda was also included. A total of 6,689 orthologous genes were identified before stricter criteria for the determination of e-values, amino acid hit lengths, and identity values was applied to further reduce this list. This led to a final list of 381 core orthologous genes for B. humilis; 39 out of these genes are involved in salt and osmotic stress responses and estimations of nonsynonymous/synonymous substitution ratios for this species and A. thaliana orthologs show that these genes are under purifying selection in B. humilis. Expression of six genes was detected in B. humilis seedlings under salt and osmotic stress treatments. Comparable expression patterns to their counterparts in Arabidopsis suggest that these orthologous genes are both sequence and functional conservation. The results of this study demonstrate that the environmental adaptations of B. humilis are mainly the results of preexisting genetic components. Future work will be required to characterize the expression patterns of these orthologous genes in natural populations and will provide further insights into the adaptive mechanisms underlying the wide range of B. humilis adaptations.
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Lei DJ, Zhao G, Xie P, Li Y, Yuan H, Zou M, Niu JG, Ma XF. Analysis of genetic diversity of Leuciscus leuciscus baicalensis using novel microsatellite markers with cross-species transferability. GENETICS AND MOLECULAR RESEARCH 2017; 16:gmr-16-02-gmr.16029376. [PMID: 28481399 DOI: 10.4238/gmr16029376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We used next-generation sequencing technology to characterize 19 genomic simple sequence repeat (SSR) markers and 11 expressed sequence tag (EST) SSR markers from Leuciscus leuciscus baicalensis, a small freshwater fish that is widely distributed in Xinjiang, China. Primers were used to test for polymorphisms in three L. leuciscus baicalensis populations in Xinjiang. There were 4-27 (average 11.3) alleles (NA), the expected heterozygosity (HE) was 0.36-0.94 (average 0.75 ± 0.14), the observed heterozygosity (HO) was 0.37-1.00 (average 0.68 ± 0.18), and the polymorphism information content (PIC) was 0.31-0.93 (average 0.71). The averages of HE and PIC for the EST-SSR markers were slightly lower than for the genomic SSR markers. Genetic analysis of the three populations showed similar results for PIC, HE, and NA. Amplifications were performed in nine other species; the top three transferability values were for Rutilus lacustris (80%), Leuciscus idus (76.7%), and Phoxinus ujmonensis (63.3%), with the following average values: PIC (0.56, 4.46, and 0.52); NA (0.40, 3.00, and 0.32); and HO (0.44, 2.74, and 0.22), respectively. L. leuciscus baicalensis is one of the most important commercial fish in Xinjiang, but in recent years, fishery resources have decreased sharply owing to water conservation projects, unreasonable utilization, and invasion by alien species. These novel SSR markers are appropriate for studies involving fingerprinting, gene flow, genetic diversity, population structure, and molecular-assisted breeding, and could contribute to the conservation of L. leuciscus baicalensis.
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Zhao P, Zhang J, Qian C, Zhou Q, Zhao X, Chen G, Ma XF. SNP Discovery and Genetic Variation of Candidate Genes Relevant to Heat Tolerance and Agronomic Traits in Natural Populations of Sand Rice ( Agriophyllum squarrosum). FRONTIERS IN PLANT SCIENCE 2017; 8:536. [PMID: 28439286 PMCID: PMC5383723 DOI: 10.3389/fpls.2017.00536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/27/2017] [Indexed: 05/24/2023]
Abstract
The extreme stress tolerance and high nutritional value of sand rice (Agriophyllum squarrosum) make it attractive for use as an alternative crop in response to concerns about ongoing climate change and future food security. However, a lack of genetic information hinders understanding of the mechanisms underpinning the morphological and physiological adaptations of sand rice. In the present study, we sequenced and analyzed the transcriptomes of two individuals representing semi-arid [Naiman (NM)] and arid [Shapotou (SPT)] sand rice genotypes. A total of 105,868 pairwise single nucleotide polymorphisms (SNPs) distributed in 24,712 Unigenes were identified among SPT and NM samples; the average SNP frequency was 0.3% (one SNP per 333 base pair). Characterization of gene annotation demonstrated that variations in genes involved in DNA recombination were associated with the survival of the NM population in the semi-arid environment. A set of genes predicted to be relevant to heat stress response and agronomic traits was functionally annotated using the accumulated knowledge from Arabidopsis and several crop plants, including rice, barley, maize, and sorghum. Four candidate genes related to heat tolerance (heat-shock transcription factor, HsfA1d), seed size (DA1-Related, DAR1), and flowering (early flowering 3, ELF3 and late elongated hypocotyl, LHY) were subjected to analysis of the genetic diversity in 10 natural populations, representing the core germplasm resource across the area of sand rice distribution in China. Only one SNP was detected in each of HsfA1d and DAR1, among 60 genotypes, with two in ELF3 and four in LHY. Nucleotide diversity ranged from 0.00032 to 0.00118. Haplotype analysis indicated that the NM population carried a specific allele for all four genes, suggesting that divergence has occurred between NM and other populations. These four genes could be further analyzed to determine whether they are associated with phenotype variation and identify alleles favorable for sand rice breeding.
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Qian C, Yin H, Shi Y, Zhao J, Yin C, Luo W, Dong Z, Chen G, Yan X, Wang XR, Ma XF. Population dynamics of Agriophyllum squarrosum, a pioneer annual plant endemic to mobile sand dunes, in response to global climate change. Sci Rep 2016; 6:26613. [PMID: 27210568 PMCID: PMC4876407 DOI: 10.1038/srep26613] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 05/04/2016] [Indexed: 12/02/2022] Open
Abstract
Climate change plays an important role in the transition of ecosystems. Stratigraphic investigations have suggested that the Asian interior experienced frequent transitions between grassland and desert ecosystems as a consequence of global climate change. Using maternally and bi-parentally inherited markers, we investigated the population dynamics of Agriophyllum squarrosum (Chenopodiaceae), an annual pioneer plant endemic to mobile sand dunes. Phylogeographic analysis revealed that A. squarrosum could originate from Gurbantunggut desert since ~1.6 Ma, and subsequently underwent three waves of colonisation into other deserts and sandy lands corresponding to several glaciations. The rapid population expansion and distribution range shifts of A. squarrosum from monsoonal climate zones suggested that the development of the monsoonal climate significantly enhanced the population growth and gene flow of A. squarrosum. These data also suggested that desertification of the fragile grassland ecosystems in the Qinghai-Tibetan Plateau was more ancient than previously suggested and will be aggravated under global warming in the future. This study provides new molecular phylogeographic insights into how pioneer annual plant species in desert ecosystems respond to global climate change, and facilitates evaluation of the ecological potential and genetic resources of future crops for non-arable dry lands to mitigate climate change.
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Zhao P, Zhang J, Zhao X, Chen G, Ma XF. Different Sets of Post-Embryonic Development Genes Are Conserved or Lost in Two Caryophyllales Species (Reaumuria soongorica and Agriophyllum squarrosum). PLoS One 2016; 11:e0148034. [PMID: 26815143 PMCID: PMC4729483 DOI: 10.1371/journal.pone.0148034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/12/2016] [Indexed: 11/23/2022] Open
Abstract
Reaumuria soongorica and sand rice (Agriophyllum squarrosum) belong to the clade of Caryophyllales and are widely distributed in the desert regions of north China. Both plants have evolved many specific traits and adaptation strategies to cope with recurring environmental threats. However, the genetic basis that underpins their unique traits and adaptation remains unknown. In this study, the transcriptome data of R. soongorica and sand rice were compared with three other species with previously sequenced genomes (Arabidopsis thaliana, Oryza sativa, and Beta vulgaris). Four different gene sets were identified, namely, the genes conserved in both species, those lost in both species, those conserved in R. soongorica only, and those conserved in sand rice only. Gene ontology showed that post-embryonic development genes (PEDGs) were enriched in all gene sets, and different sets of PEDGs were conserved or lost in both the R. soongorica and sand rice genomes. Expression profiles of Arabidopsis orthologs further provided some clues to the function of the species-specific conserved PEDGs. Such orthologs included LEAFY PETIOLE, which could be a candidate gene involved in the development of branch priority in sand rice.
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Zhao P, Zhang J, Zhao X, Chen G, Ma XF. Different Sets of Post-Embryonic Development Genes Are Conserved or Lost in Two Caryophyllales Species (Reaumuria soongorica and Agriophyllum squarrosum). PLoS One 2016. [PMID: 26815143 DOI: 10.1371/journal.pone.0148034.g001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
Reaumuria soongorica and sand rice (Agriophyllum squarrosum) belong to the clade of Caryophyllales and are widely distributed in the desert regions of north China. Both plants have evolved many specific traits and adaptation strategies to cope with recurring environmental threats. However, the genetic basis that underpins their unique traits and adaptation remains unknown. In this study, the transcriptome data of R. soongorica and sand rice were compared with three other species with previously sequenced genomes (Arabidopsis thaliana, Oryza sativa, and Beta vulgaris). Four different gene sets were identified, namely, the genes conserved in both species, those lost in both species, those conserved in R. soongorica only, and those conserved in sand rice only. Gene ontology showed that post-embryonic development genes (PEDGs) were enriched in all gene sets, and different sets of PEDGs were conserved or lost in both the R. soongorica and sand rice genomes. Expression profiles of Arabidopsis orthologs further provided some clues to the function of the species-specific conserved PEDGs. Such orthologs included LEAFY PETIOLE, which could be a candidate gene involved in the development of branch priority in sand rice.
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Yan X, Zhou M, Dong X, Zou S, Xiao H, Ma XF. Molecular mechanisms of foliar water uptake in a desert tree. AOB PLANTS 2015; 7:plv129. [PMID: 26567212 PMCID: PMC4685171 DOI: 10.1093/aobpla/plv129] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 10/29/2015] [Indexed: 05/22/2023]
Abstract
Water deficits severely affect growth, particularly for the plants in arid and semiarid regions of the world. In addition to precipitation, other subsidiary water, such as dew, fog, clouds and small rain showers, may also be absorbed by leaves in a process known as foliar water uptake. With the severe scarcity of water in desert regions, this process is increasingly becoming a necessity. Studies have reported on physical and physiological processes of foliar water uptake. However, the molecular mechanisms remain less understood. As major channels for water regulation and transport, aquaporins (AQPs) are involved in this process. However, due to the regulatory complexity and functional diversity of AQPs, their molecular mechanism for foliar water uptake remains unclear. In this study, Tamarix ramosissima, a tree species widely distributed in desert regions, was investigated for gene expression patterns of AQPs and for sap flow velocity. Our results suggest that the foliar water uptake of T. ramosissima occurs in natural fields at night when the humidity is over a threshold of 85 %. The diurnal gene expression pattern of AQPs suggests that most AQP gene expressions display a circadian rhythm, and this could affect both photosynthesis and transpiration. At night, the PIP2-1 gene is also upregulated with increased relative air humidity. This gene expression pattern may allow desert plants to regulate foliar water uptake to adapt to extreme drought. This study suggests a molecular basis of foliar water uptake in desert plants.
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Zhang JK, Ma XF, Wang XW, Cai JQ, Wu XL, Niu YP, Zhou N, Hua RM. X-ray structure and conformational study of tris(2-(dimethylamino)phenyl)methanol salt derivatives: Roles of anions and hydrogen bond. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.07.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Ma XF, Xu FL, Gao LF, Wang YX, Pan ZB. Effect of age on the immune system and pathology of mice with chronic graft-versus-host disease lupus nephritis. GENETICS AND MOLECULAR RESEARCH 2015; 14:10999-1005. [PMID: 26400329 DOI: 10.4238/2015.september.21.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We investigated the effect of age on the expression of immune molecules [ANA, C4, double stranded DNA (dsDNA), CD16/32, CD19, CD3, and CD64], urine protein, and pathology in mice with chronic graft-versus-host disease (cGVHD) lupus nephritis (LN), and their relationship with reactivity index score. Mouse models of cGVHD LN were established, and mice were randomly divided into four aged-based groups of nine mice each. Serum levels of ANA, C4, and dsDNA were determined, the urine protein levels were assessed, and expression levels of CD16/32, CD19, CD3, and CD64 were measured. Expression levels of CD16/32+CD19(T1), CD16/CD32+CD3(T2), and CD64+CD3 or CD19(T3) were defined in the thymus, in bone marrow they were defined as CD16/32+CD19(B1), CD16/32+CD3(B2), CD64+CD3 or CD19(B3), and in spleen they were defined as CD16/32+CD19(P1), CD16/32+CD3(P2), CD64+CD3 or CD19(P3), respectively. There were significant differences in the levels of dsDNA and urine protein among the four groups (P < 0.05), which were negatively correlated with age. B1, B2, S1, and S2 were significantly different among the four groups (P < 0.05), with a positive correlation with age for B1 and B2. There was no correlation of expression of ANA, C4, dsDNA, T1-T3, B1-B3, S2-S3 with reactivity index score; S1 was the exception (r = -0.440, P = 0.011). Age influenced levels of dsDNA and urine protein in the mouse cGVHD model of LN. S1 was associated with reactivity index score and might also affect pathological changes.
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Niu YP, Zhang JK, Wang XW, Ma XF, Cai JQ, Zhou N, Zheng ZW, Hua RM. X-ray structure and conformational study of tris(2-(dimethylamino)phenyl)methanol: Roles of hydrogen bond in conformational conversions of molecules. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Zhao P, Capella-Gutiérrez S, Shi Y, Zhao X, Chen G, Gabaldón T, Ma XF. Transcriptomic analysis of a psammophyte food crop, sand rice (Agriophyllum squarrosum) and identification of candidate genes essential for sand dune adaptation. BMC Genomics 2014; 15:872. [PMID: 25287394 PMCID: PMC4459065 DOI: 10.1186/1471-2164-15-872] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 09/29/2014] [Indexed: 12/22/2022] Open
Abstract
Background Sand rice (Agriophyllum squarrosum) is an annual desert plant adapted to
mobile sand dunes in arid and semi-arid regions of Central Asia. The sand rice
seeds have excellent nutrition value and have been historically consumed by local
populations in the desert regions of northwest China. Sand rice is a potential
food crop resilient to ongoing climate change; however, partly due to the scarcity
of genetic information, this species has undergone only little agronomic
modifications through classical breeding during recent years. Results We generated a deep transcriptomic sequencing of sand rice, which uncovers 67,741
unigenes. Phylogenetic analysis based on 221 single-copy genes showed close
relationship between sand rice and the recently domesticated crop sugar beet.
Transcriptomic comparisons also showed a high level of global sequence
conservation between these two species. Conservation of sand rice and sugar beet
orthologs assigned to response to salt stress gene ontology term suggests that
sand rice is also a potential salt tolerant plant. Furthermore, sand rice is far
more tolerant to high temperature. A set of genes likely relevant for resistance
to heat stress, was functionally annotated according to expression levels,
sequence annotation, and comparisons corresponding transcriptome profiling results
in Arabidopsis. Conclusions The present work provides abundant genomic information for functional dissection
of the important traits in sand rice. Future screening the genetic variation among
different ecotypes and constructing a draft genome sequence will further
facilitate agronomic trait improvement and final domestication of sand rice. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-872) contains supplementary material, which is available to authorized users.
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Lind M, Källman T, Chen J, Ma XF, Bousquet J, Morgante M, Zaina G, Karlsson B, Elfstrand M, Lascoux M, Stenlid J. A Picea abies linkage map based on SNP markers identifies QTLs for four aspects of resistance to Heterobasidion parviporum infection. PLoS One 2014; 9:e101049. [PMID: 25036209 PMCID: PMC4103950 DOI: 10.1371/journal.pone.0101049] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 06/03/2014] [Indexed: 02/05/2023] Open
Abstract
A consensus linkage map of Picea abies, an economically important conifer, was constructed based on the segregation of 686 SNP markers in a F1 progeny population consisting of 247 individuals. The total length of 1889.2 cM covered 96.5% of the estimated genome length and comprised 12 large linkage groups, corresponding to the number of haploid P. abies chromosomes. The sizes of the groups (from 5.9 to 9.9% of the total map length) correlated well with previous estimates of chromosome sizes (from 5.8 to 10.8% of total genome size). Any locus in the genome has a 97% probability to be within 10 cM from a mapped marker, which makes the map suited for QTL mapping. Infecting the progeny trees with the root rot pathogen Heterobasidion parviporum allowed for mapping of four different resistance traits: lesion length at the inoculation site, fungal spread within the sapwood, exclusion of the pathogen from the host after initial infection, and ability to prevent the infection from establishing at all. These four traits were associated with two, four, four and three QTL regions respectively of which none overlapped between the traits. Each QTL explained between 4.6 and 10.1% of the respective traits phenotypic variation. Although the QTL regions contain many more genes than the ones represented by the SNP markers, at least four markers within the confidence intervals originated from genes with known function in conifer defence; a leucoanthocyanidine reductase, which has previously been shown to upregulate during H. parviporum infection, and three intermediates of the lignification process; a hydroxycinnamoyl CoA shikimate/quinate hydroxycinnamoyltransferase, a 4-coumarate CoA ligase, and a R2R3-MYB transcription factor.
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Niu YP, Wang XW, Zheng ZW, Ma XF, Cai JQ, Zhang JK, Cheng JL. Vinyl polymerization of norbornene catalyzed by 2-Py-amidine Ni(II) complex/methylaluminoxane systems. Appl Organomet Chem 2014. [DOI: 10.1002/aoc.3183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Feng Q, Yu MZ, Wang JC, Hou WJ, Gao LY, Ma XF, Pei XW, Niu YJ, Liu XY, Qiu C, Pang WH, Du LL, Zhang Q. Synergistic inhibition of breast cancer by co-delivery of VEGF siRNA and paclitaxel via vapreotide-modified core-shell nanoparticles. Biomaterials 2014; 35:5028-38. [PMID: 24680191 DOI: 10.1016/j.biomaterials.2014.03.012] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/07/2014] [Indexed: 01/05/2023]
Abstract
A somatostatin analog, vapreotide (VAP), can be used as a ligand for targeting drug delivery based on its high affinity to somatostatin receptors (SSTRs), which is overexpressed in many tumor cells. RNA interference plays an important role on downregulation of vascular endothelial growth factor (VEGF), which is important for tumor growth, progression and metastasis. To improve tumor therapy efficacy, the vapreotide-modified core-shell type nanoparticles co-encapsulating VEGF targeted siRNA (siVEGF) and paclitaxel (PTX), termed as VAP-PLPC/siRNA NPs, were developed in this study. When targeted via somatostatin receptors to tumor cells, the VAP-PLPC/siRNA NPs could simultaneously delivery siVEGF and PTX into cells and achieve a synergistic inhibition of tumor growth. Interestingly, in vitro cell uptake and gene silencing experiments demonstrated that the targeted VAP-PLPC/siRNA NPs exhibited significant higher intracellular siRNA accumulation and VEGF downregulation in human breast cancer MCF-7 cells, compared to those of the non-targeted PEG-PLPC/siRNA NPs. More importantly, in vivo results further demonstrated that the targeted VAP-PLPC/siRNA NPs had significant stronger drug distribution in tumor tissues and tumor growth inhibition efficacy via receptor-mediated targeting delivery, accompany with an obvious inhibition of neovascularization induced by siVEGF silencing. These results suggested that the co-delivery of siRNA and paclitaxel via vapreotide-modified core-shell nanoparticles would be a promising approach for tumor targeted therapy.
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Gao LY, Liu XY, Chen CJ, Wang JC, Feng Q, Yu MZ, Ma XF, Pei XW, Niu YJ, Qiu C, Pang WH, Zhang Q. Core-Shell type lipid/rPAA-Chol polymer hybrid nanoparticles for in vivo siRNA delivery. Biomaterials 2014; 35:2066-78. [DOI: 10.1016/j.biomaterials.2013.11.046] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 11/18/2013] [Indexed: 11/26/2022]
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Shi Y, Yan X, Zhao P, Yin H, Zhao X, Xiao H, Li X, Chen G, Ma XF. Transcriptomic analysis of a tertiary relict plant, extreme xerophyte Reaumuria soongorica to identify genes related to drought adaptation. PLoS One 2013; 8:e63993. [PMID: 23717523 PMCID: PMC3662755 DOI: 10.1371/journal.pone.0063993] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 04/08/2013] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Reaumuria soongorica is an extreme xerophyte shrub widely distributed in the desert regions including sand dune, Gobi and marginal loess of central Asia which plays a crucial role to sustain and restore fragile desert ecosystems. However, due to the lacking of the genomic sequences, studies on R. soongorica had mainly limited in physiological responses to drought stress. Here, a deep transcriptomic sequencing of R. soongorica will facilitate molecular functional studies and pave the path to understand drought adaptation for a desert plant. METHODOLOGY/PRINCIPAL FINDINGS A total of 53,193,660 clean paired-end reads was generated from the Illumina HiSeq™ 2000 platform. By assembly with Trinity, we got 173,700 contigs and 77,647 unigenes with mean length of 677 bp and N50 of 1109 bp. Over 55% (43,054) unigenes were successfully annotated based on sequence similarity against public databases as well as Rfam and Pfam database. Local BLAST and Kyoto Encyclopedia of Genes and Genomes (KEGG) maps were used to further exhausting seek for candidate genes related to drought adaptation and a set of 123 putative candidate genes were identified. Moreover, all the C4 photosynthesis genes existed and were active in R. soongorica, which has been regarded as a typical C3 plant. CONCLUSION/SIGNIFICANCE The assembled unigenes in present work provide abundant genomic information for the functional assignments in an extreme xerophyte R. soongorica, and will help us exploit the genetic basis of how desert plants adapt to drought environment in the near future.
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Chen CJ, Wang JC, Zhao EY, Gao LY, Feng Q, Liu XY, Zhao ZX, Ma XF, Hou WJ, Zhang LR, Lu WL, Zhang Q. Self-assembly cationic nanoparticles based on cholesterol-grafted bioreducible poly(amidoamine) for siRNA delivery. Biomaterials 2013; 34:5303-16. [PMID: 23570718 DOI: 10.1016/j.biomaterials.2013.03.056] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 03/18/2013] [Indexed: 12/20/2022]
Abstract
In this study, a series of bioreducible poly(amidoamine)s grafting different percentages of cholesterol (rPAA-Ch14: 14%, rPAA-Ch29: 29%, rPAA-Ch57: 57% and rPAA-Ch87: 87%) was synthesized and used for siRNA delivery. These amphiphilic polymers were able to self-assemble into cationic nanoparticles in aqueous solution at low concentrations. The nanoparticle formation was evidenced via cryo-transmission electron microscope (Cryo-TEM) and dynamic light scattering analysis. The average hydrodynamic size of rPAA-Ch blank nanoparticles was about 80-160 nm with zeta potential of 50-60 mV. Also, the effects of different percentages of cholesterol grafted onto rPAA on physicochemical characteristics, in vitro cytotoxicity, cellular uptake, VEGF gene silencing efficacy and translocation mechanism of rPAA-Ch/siRNA complexes were investigated. The results showed that rPAA-Ch57 polymer was not only able to form stable nanocomplexes and possess high cell uptake, but also to exhibit the best in vitro VEGF gene silencing efficacy and the best in vivo tumor growth inhibition effect when it was formulated with VEGF-siRNA. Moreover, the observations of confocal laser scanning microscope (CLSM) and the study of cholesterol competitive inhibition demonstrated that endosomal/lysosomal escape and cytoplasmic dissociation of rPAA-Ch57/siRNA complexes were dependent on the "proton sponge effect" and disulfide cleavage, following internalization with cholesterol-related endocytosis pathway and subsequent transportion into endosomes/lysosomes. These findings indicated that the rPAA-Ch57 polymer should be a promising and potent carrier for siRNA delivery.
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Di CX, Yang LN, Zhang H, An LZ, Zhang X, Ma XF, Sun C, Wang XH, Yang R, Wu ZH, Si J. Effects of carbon-ion beam or X-ray irradiation on anti-apoptosis ΔNp73 expression in HeLa cells. Gene 2012; 515:208-13. [PMID: 23228853 DOI: 10.1016/j.gene.2012.11.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 10/30/2012] [Accepted: 11/01/2012] [Indexed: 01/16/2023]
Abstract
ΔNp73 has emerged as an interesting novel factor in cancer research. Here, we report the effect of carbon-ion beams on ΔNp73 expression in human cervix carcinoma HeLa cells in contrast to the effect of X-rays. Cellular sensitivities were determined by colony formation. Radiation-induced cell cycle arrest was investigated with flow cytometry. Additionally, radiation-induced apoptosis was analyzed with flow cytometry and Hoechst staining. Furthermore, ΔNp73 expression was examined by semi-quantitative reverse transcription-PCR (semi-quantitative RT-PCR) as well as by Western blot analysis. Following irradiation, stronger G2/M phase arrest, more significant increase in apoptosis and more pronounced ΔNp73 degradation were observed after exposure to high-LET carbon beams in comparison with X-rays at 4 Gy doses. These observations indicate that there is a differential ΔNp73 expression in response to different LET radiations, and down-regulated ΔNp73 expression might play a critical role in promoting cycle arrest and apoptosis in cancer cells. This study highlights the potential of ΔNp73 in radiotherapy.
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Abstract
Perennial plants monitor seasonal changes through changes in environmental conditions such as the quantity and quality of light and genes in the photoperiodic pathway are known to be involved in controlling these processes. Here, we examine 25 of genes from the photoperiod pathway in Populus tremula (Salicaceae) for signatures of adaptive evolution. Overall, levels of synonymous polymorphism in the 25 genes are lower than at control loci selected randomly from the genome. This appears primarily to be caused by lower levels of synonymous polymorphism in genes associated with the circadian clock. Natural selection appears to play an important role in shaping protein evolution at several of the genes in the photoperiod pathways, which is highlighted by the fact that approximately 40% of the genes from the photoperiod pathway have estimates of selection on nonsynonymous polymorphisms that are significantly different from zero. A surprising observation we make is that circadian clock-associated genes appear to be over-represented among the genes showing elevated rates of protein evolution; seven genes are evolving under positive selection and all but one of these genes are involved in the circadian clock of Populus.
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Zhu M, Chai G, Zhang Y, Ma XF, Yu ZY, Zhu YJ. [Registration technology for mandibular angle osteotomy based on augmented reality]. SHANGHAI KOU QIANG YI XUE = SHANGHAI JOURNAL OF STOMATOLOGY 2010; 19:571-574. [PMID: 21431251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PURPOSE To establish an effective path to register the operative plan to the real model of mandible made by rapid prototyping (RP) technology. METHODS Computerize tomography (CT) was performed on 20 patients to create 3D images, and computer aided operation planning information can be merged with the 3D images. Then dental cast was used to fix the signal which can be recognized by the software. The dental cast was transformed to 3D data with a laser scanner and a programmer that run on a personal computer named Rapidform matching the dental cast and the mandible image to generate the virtual image. Then the registration was achieved by video monitoring system. RESULTS By using this technology, the virtual image of mandible and the cutting planes both can overlay the real model of mandible made by RP. CONCLUSIONS This study found an effective way for registration by using dental cast, and this way might be a powerful option for the registration of augmented reality. Supported by Program for Innovation Research Team of Shanghai Municipal Education Commission.
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Zhu M, Chai G, Zhang Y, Ma XF, Yu ZY, Mu XZ, Qi ZL. [The morphological study on masseter muscle following mandibular angle osteotomy]. ZHONGHUA ZHENG XING WAI KE ZA ZHI = ZHONGHUA ZHENGXING WAIKE ZAZHI = CHINESE JOURNAL OF PLASTIC SURGERY 2010; 26:340-344. [PMID: 21174787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
OBJECTIVE To evaluate the morphological change of masseter after the mandibular angle osteotomy. METHODS Computerized tomography (CT) examination was performed on 120 patients treated by mandibular angle osteotomy before operation and at 3, 6, 12 months after operation, respectively. The pre- and postoperative masseter muscle thickness and cross-sectional area were evaluated using 3D CT images observed from 3 selected slice planes, which were paralleled with Frankfurt horizontal plane. These CT images were stored and three-dimensional reconstruction were made for calculation of masseter muscle volume through software. RESULTS After operation, the reduction of the masseter muscle volume and cross-sectional area was seen. The volume of the masseter at 3, 6, 12 months postoperatively decreased to 82.02%, 77.00% and 80.43% (P < 0.05). The cross-sectional area at 3, 6,12 months postoperatively decreased to 85.81%, 78.86% and 81.56% at A plane, 80.94%, 75.03% and 77.04% at B plane, and reached to 13.46%, 11.48% and 13.89% at C plane (P < 0.05, P < 0.05, P < 0.01). The masseter thickness after operation was significantly different from that before operation during the follow-up period, but not at 12 months after operation at A plane. CONCLUSIONS The masseter atrophy happens spontaneously after mandibular angle osteotomy, especially at the region of mandibular angle. It should be considered during surgical design.
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Xiao M, An L, Yang X, Ge X, Qiao H, Zhao T, Ma X, Fan J, Zhu M, Dou Z. Establishing a human pancreatic stem cell line and transplanting induced pancreatic islets to reverse experimental diabetes in rats. ACTA ACUST UNITED AC 2008; 51:779-88. [DOI: 10.1007/s11427-008-0109-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 07/10/2008] [Indexed: 11/29/2022]
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Rizza S, Catara A, Ma XF, Deng Z. Detection of Multiple Infections of Citrus exocortis viroid, Citrus viroid III, and Hop stunt viroid Variants in Hunan Province, China. PLANT DISEASE 2007; 91:1205. [PMID: 30780682 DOI: 10.1094/pdis-91-9-1205a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Citrus cultivation in China has increased since the late 1970s, with China now having the largest area of citrus in culture in the world that is spread in 22 provinces and municipalities. Hunan Province has undergone a program to become one of the major citrus producers in China. Poncirus trifoliata is the main rootstock, so citrus viroids are a limiting factor for further citriculture development. In mainland China, only the presence of Citrus exocortis viroid (CEVd) has been reported from Etrog citron indexing, sPAGE (sequential polyacrylamide gel electrophoresis) analysis (2), and reverse transcription (RT)-PCR (3). Three viroid-like RNAs, a1, b1, and d, based on sPAGE patterns were detected years ago in our laboratory in budsticks received from Sichuan Province. To identify different viroids and determine their distribution, a survey has been undertaken. Field trees showing stunting, bark scaling and cracking of the rootstock, and poor yield were tested using biological indexing and PCR for the most frequent citrus viroids. Samples from six trees of a local sweet orange variety and three of a Clementine variety introduced from abroad, both grafted on P. trifoliata and showing a variable degree of bark scaling and cracking, were collected near Changsha and in the County of Xin Ning at the end of summer 2006. Small pieces of bark were inserted in stems of young E. citron budwood grafted on rough lemon and maintained in a warm greenhouse (24 to 32°C). Indexing on E. citron showed mild epinasty and leaf roll typical of citrus viroid infections. To identify specific viroids, bark was ground to a fine powder with liquid nitrogen and total RNA was extracted with TRIZOL Reagent (Invitrogen, San Diego, CA) and tested by RT-PCR to detect CEVd, Hop Stunt viroid (HSVd), and Citrus viroid III (CVd-III), as well as to identify the cachexia variants of HSVd. Four primer pairs were used to test the RNA extracts by RT-PCR (1). All samples were infected by HSVd, eight with CVd-III, and six with CEVd. The cachexia variants of HSVd were detected in four of nine samples. Mixed infections were as follows: one sample had CEVd and HSVd, eight had HSVd and CVd-III, and five were infected by the three viroids. A second sampling 3 months after inoculation gave the same amplification patterns. The results show that at least three viroids are present in citrus orchards in Hunan Province. To our knowledge, this is the first report of cachexia variants of HSVd and CVd-III in China. The common occurrence of these viroids supports the need for proper indexing of mother trees and a specific shoot tip grafting program to create healthy budwood sources to provide healthy plants. References: (1) L. Bernard and N. Duran-Vila. Mol. Cell. Probes, 20:105, 2006. (2) L. Han et al. Viroids. CSIRO Publishing, Melbourne, 283, 2003. (3). Q. Hu et al. Acta Bot. Sin. 39:613, 1997.
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Dong J, Wang QX, Zhou CY, Ma XF, Zhang YC. Activation of the STAT1 signalling pathway in lupus nephritis in MRL/lpr mice. Lupus 2007; 16:101-9. [PMID: 17402366 DOI: 10.1177/0961203306075383] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Interferons (IFNs), type I (alpha/beta) and type II (gamma), comprise a family of multifunctional cytokines with antiviral, antiproliferative and immunomodulating properties. Both type I and type II IFNs have been heavily implicated in the pathogenesis of systemic lupus erythematosus (SLE). The biological effects of IFNs are mediated through the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway in which both IFN-alpha/beta and IFN-gamma activate the transcription factor STAT1. However, little is known about the pathogenic significance of STAT1 in SLE. At this point, we examined the expression and activation of STAT1 in the kidney of MRL/lpr mice with lupus nephritis (LN) by immunohistochemistry, Western botting and real time quantitative RT-PCR. Increased levels of total STAT1 protein and its activated/phosphorylated form were detected in kidney samples from MRL/lpr mice with LN as compared to those from control mice. Phosphorylated STAT1 was predominantly detected in glomeruli cells. Gene expression of the STAT induced feedback inhibitors suppressor of cytokine signalling-1 (SOCS-1) and SOCS-3 was also enhanced in MRL/lpr mice. In MRL/lpr mesangial cells, both IFN-alpha and IFN-gamma rapidly induced the phosphorylation of STAT in vitro. Our results demonstrate that expression and activation of STAT1 are significantly increased in murine lupus nephritis, and indicate that STAT1 signalling pathway may play an important role in the pathogenesis of kidney inflammation.
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Yang JH, Yu JG, Ma XF. Preparation and properties of ethylenebisformamide plasticized potato starch (EPTPS). Carbohydr Polym 2006. [DOI: 10.1016/j.carbpol.2005.08.059] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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