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2.
Mol Med Rep ; 21(2): 649-658, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31974626

RESUMO

Osteosarcoma (OS) is the most common type of primary malignant bone tumor, which has a high incidence rate in children and adolescents. This research aims to reveal the role of long intergenic non­protein coding RNA 00460 (LINC00460) in OS by the loss­of­function experiment. LINC00460 is involved in the development of multiple types of tumor, but the role of LINC00460 in OS is unclear. To discover more effective molecular targets for the treatment of OS, the association between LINC00460 and OS prognosis was analyzed using the Gene Expression Profiling Interactive Analysis database. Additionally, small interfering RNA was used to knockdown LINC00460 gene expression in vitro to verify its biological effects on the viability, invasive and migratory potential of OS cells. LINC00460 knockdown significantly reduced the viability of OS cells and initiated cell cycle arrest within the G0/G1 phase through the decreased expression of cyclin D1 and CDK4/CDK6. In addition, LINC00460 knockdown promoted apoptosis of OS cells, and inhibited the migratory and invasive abilities of OS cells through the inhibition of the epithelial­mesenchymal transition pathway. In conclusion, the present study reported that LINC00460 may predict OS prognosis, and may serve an important role in mediating the viability, invasive and migratory potential of OS cells. Based on these findings, LINC00460 demonstrated promising potential as a future therapeutic target for OS treatment.

3.
Environ Sci Pollut Res Int ; 26(28): 29003-29011, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31388952

RESUMO

Cadmium (Cd) re-mobilize by phosphate-solubilizing bacteria (PSB) from immobilization contaminated soil has drawn great attention due to its serious threat to human health through food chain. However, Cd binding with weathered coal (WC), an effective Cd immobilization material, will be re-mobilized by PSB or not is still unclear. In this study, the soil and sand pots with Cd were respectively mixed with the weight fractions of 0‰, 2‰, and 3‰ WC, inoculated with or without PSB, and planted with Amaranthus mangostanus L. The experimental results indicated that: (i) Cd in soil was transformed into organic fraction with WC, which has been led to the Cd accumulation concentrations in roots and shoots reduced by 38.8% and 20.5%, respectively; (ii) PSB could promote the concentration of exchangeable-Cd fraction and soil Cd uptake by amaranth in all treatments; and (iii) WC application in sand pot respectively reduced the Cd accumulation by 47.5% in roots and 24.1% in shoots, but PSB inoculation showed no significant effect on Cd accumulation in plants under WC application. SEM, zeta potential, and FT-IR results showed that PSB inoculation after Cd immobilized by WC had no influence on the microstructure, amount of negative charge, type, and content of functional groups in WC, indicating that organic fraction Cd in WC was not re-mobilized by PSB. Therefore, the application of WC in contaminated soil was conducive to transforming Cd in organic-bound forms and intensifying Cd immobilization effects.


Assuntos
Amaranthus/metabolismo , Bactérias/metabolismo , Cádmio/análise , Carvão Mineral , Fosfatos/química , Solo/química , Poluição Ambiental , Raízes de Plantas/metabolismo , Espectroscopia de Infravermelho com Transformada de Fourier , Tempo (Meteorologia)
4.
Front Oncol ; 9: 516, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31275851

RESUMO

DNA replication is precisely regulated in cells and its dysregulation can trigger tumorigenesis. Here we identified that the TOPBP1 interacting checkpoint and replication regulator (TICRR) mRNA level was universally and highly expressed in 15 solid cancer types. Depletion of TICRR significantly inhibited tumor cell growth, colony formation and migration in vitro, and strikingly inhibited tumor growth in the xenograft model. We reveal that knockdown of TICRR inhibited not only the initiation but also the fork progression of DNA replication. Suppression of DNA synthesis by TICRR silencing caused DNA damage accumulation, subsequently activated the ATM/CHK2 dependent p53 signaling, and finally induced cell cycle arrest and apoptosis at least in p53-wild cancer cells. Further, we show that a higher TICRR level was associated with poorer overall survival (OS) and disease free survival (DFS) in multiple cancer types. In conclusion, our study shows that TICRR is involved in tumorigenesis by regulating DNA replication, acting as a common biomarker for cancer prognosis and could be a promising target for drug-development and cancer treatment.

5.
Ecotoxicol Environ Saf ; 181: 265-273, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31201958

RESUMO

The application of palygorskite (PAL) for potentially toxic trace elements (Cd2+, Ni2+, etc.) remediation in polluted soil can substantially reduce the bioavailability and toxicity of these hazard materials. However, the secretion of organic acids and siderophores by microorganisms might result in the re-mobilization of cadmium (Cd) in PAL-bound forms (PAL-Cd). In this study, the interactive effects between Cd stabilized by PAL and mobilized by siderophores from Pseudomonas fluorescens were performed with four flask-shaking experimental treatments, namely, strain with or without an ability of siderophores production respectively associated with or without PAL-Cd. The GC-MS and UHPLC-MS test methods were used to analyze the concentrations of metabolites. Results showed that the Cd mobilized by strain with siderophores production was 22.1% higher than that of strain without the ability of siderophores production (p < 0.05). The mobilization of Cd in PAL in turn significantly reduced the siderophores production of Pseudomonas fluorescens by 25.1% (p < 0.05). The numbers of metabolites significantly up-regulated and down-regulated were 9 and 22 in strain groups with PAL-Cd addition compared with the groups without PAL-Cd, respectively. Metabolomics analysis revealed that the mobilized Cd affects the signal transduction pathway and primary metabolic processes, reduces the metabolic capacity of pentose phosphate pathway, glycolysis and tricarboxylic acid cycle pathway. These changes inhibit the ability of strain to biosynthesize amino acids during the mobilization processes, further reducing the capacity of Pseudomonas fluorescens to produce siderophores. This study provides a useful information on how to select soil Cd-stabilizing materials in a targeted manner and how to avoid Cd re-mobilization by siderophores.


Assuntos
Cádmio/análise , Compostos de Magnésio , Pseudomonas fluorescens/metabolismo , Sideróforos/metabolismo , Compostos de Silício , Poluentes do Solo/análise
6.
J Environ Manage ; 244: 453-461, 2019 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-31154108

RESUMO

Biogas slurry (BS) is a main byproduct of biogas production that is commonly used for agricultural irrigation because of its abundant nutrients and microelements. However, direct application of BS may cause quality decline and nitrate and heavy metal accumulation in crops. To address this issue, a microalgae culture experiment and an irrigation experiment were performed to evaluate the removal efficiencies of nutrients and heavy metals from diluted BS by microalgae Scenedesmus sp. and to investigate the effects of irrigation with microalgae-treated BS (MBS-25, MBS-50, MBS-75, and MBS-100) on nutritional quality, oxidation resistance, and nitrate and heavy metal residues in Chinese cabbage. After 8 days of continuous culture, a ratio of 1/1 for BS/tap water mixture (BS-50) was the optimal proportion for microalgal growth (3.73 g dry cell L-1) and efficient removal of total nitrogen (86.1%), total phosphorus (94.3%), COD (87.5%), Cr (50%), Pb (60.7%), and Cd (59.7%). The pH in MBS-50 medium recovered to the highest level in a shorter period of time and accelerated the gas stripping of ammonia nitrogen and the formation of insoluble phosphate and metals, which partly contributed to the high removal efficiencies. MBS irrigation significantly promoted crop growth; improved nutritional quality, edible taste, and oxidation resistance; and reduced nitrate and heavy metal residues in Chinese cabbage at a large scale. Therefore, microalgae culture was beneficial to reduce negative impacts of BS irrigation in crop growth and agricultural product safety. This study may provide a theoretical basis for the safe utilization of BS waste in agricultural irrigation.


Assuntos
Brassica , Metais Pesados , Microalgas , Biocombustíveis , Valor Nutritivo
7.
Cell Physiol Biochem ; 45(2): 547-557, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29402834

RESUMO

BACKGROUND/AIMS: Endothelial cell dysfunction is the principal pathological process underlying atherosclerotic cardiovascular disease. G protein-coupled receptor 124 (GPR124), an orphan receptor in the adhesion GPCR subfamily, promotes angiogenesis in the brain. In the present study, we explored the role of endothelial GPR124 in the development and progression of atherosclerosis in adult mice. METHODS: Using tetracycline-inducible transgenic systems, we generated mice expressing GPR124 specifically under control of the Tie-2 promoter. The animal model of atherosclerosis was constructed by intravenously injecting AAV-PCSK9DY into tetracycline-regulated mice and feeding the mice a high-fat diet for 16 consecutive weeks. Biochemical analysis and immunohistochemistry methods were used to address the role and mechanism of GPR124 in the pathological process of atherosclerosis. RESULTS: Higher TC (total cholesterol) and LDL-C (low density lipoprotein cholesterol) levels in serum and greater lipid deposition in the aortic sinus were found in atherosclerotic mice with GPR124 overexpression, coincident with the elevated proliferation of smooth muscle cells. We observed an elevation of ONOO- in the aortic sinus in this model by using immunofluorescence, and the experiments showed that the specific overexpression of GPR124 in the endothelium induced the up-regulation of CD68, NLRP3 and caspase-1 levels in the aortic sinus. CONCLUSION: The above results indicate that manipulating GPR124 in the endothelium may contribute to delayed pathological progression of atherosclerosis.


Assuntos
Aterosclerose/patologia , Receptores Acoplados a Proteínas-G/metabolismo , Animais , Antígenos CD/metabolismo , Antígenos de Diferenciação Mielomonocítica/metabolismo , Aterosclerose/metabolismo , Caspase 1/metabolismo , Colesterol/sangue , LDL-Colesterol/sangue , Dieta Hiperlipídica , Modelos Animais de Doenças , Humanos , Inflamação/etiologia , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Miócitos de Músculo Liso/citologia , Miócitos de Músculo Liso/efeitos dos fármacos , Miócitos de Músculo Liso/metabolismo , Proteína 3 que Contém Domínio de Pirina da Família NLR/metabolismo , Ácido Peroxinitroso/metabolismo , Plasmídeos/genética , Plasmídeos/metabolismo , Receptores Acoplados a Proteínas-G/genética , Seio Aórtico/metabolismo , Seio Aórtico/patologia
8.
Sci Rep ; 7(1): 1806, 2017 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-28496210

RESUMO

To understand the potential genetic basis of highland adaptation of fungal pathogenicity, we present here the ~116 Mb de novo assembled high-quality genome of Ophiocordyceps sinensis endemic to the Qinghai-Tibetan Plateau. Compared with other plain-dwelling fungi, we find about 3.4-fold inflation of the O. sinensis genome due to a rapid amplification of long terminal repeat retrotransposons that occurred ~38 million years ago in concert with the uplift of the plateau. We also observe massive removal of thousands of genes related to the transport process and energy metabolism. O. sinensis displays considerable lineage-specific expansion of gene families functionally enriched in the adaptability of low-temperature of cold tolerance, fungal pathogenicity and specialized host infection. We detect signals of positive selection for genes involved in peroxidase and hypoxia to enable its highland adaptation. Resequencing and analyzing 31 whole genomes of O. sinensis, representing nearly all of its geographic range, exhibits latitude-based population divergence and nature selection for population inhabitation towards higher altitudes on the Qinghai-Tibetan Plateau.


Assuntos
Genoma Fúngico , Genômica , Hypocreales/genética , Micoses/microbiologia , Biodiversidade , Biologia Computacional/métodos , Evolução Molecular , Genômica/métodos , Anotação de Sequência Molecular , Família Multigênica , Retroelementos , Sequenciamento Completo do Genoma
9.
Mol Plant ; 10(6): 866-877, 2017 06 05.
Artigo em Inglês | MEDLINE | ID: mdl-28473262

RESUMO

Tea is the world's oldest and most popular caffeine-containing beverage with immense economic, medicinal, and cultural importance. Here, we present the first high-quality nucleotide sequence of the repeat-rich (80.9%), 3.02-Gb genome of the cultivated tea tree Camellia sinensis. We show that an extraordinarily large genome size of tea tree is resulted from the slow, steady, and long-term amplification of a few LTR retrotransposon families. In addition to a recent whole-genome duplication event, lineage-specific expansions of genes associated with flavonoid metabolic biosynthesis were discovered, which enhance catechin production, terpene enzyme activation, and stress tolerance, important features for tea flavor and adaptation. We demonstrate an independent and rapid evolution of the tea caffeine synthesis pathway relative to cacao and coffee. A comparative study among 25 Camellia species revealed that higher expression levels of most flavonoid- and caffeine- but not theanine-related genes contribute to the increased production of catechins and caffeine and thus enhance tea-processing suitability and tea quality. These novel findings pave the way for further metabolomic and functional genomic refinement of characteristic biosynthesis pathways and will help develop a more diversified set of tea flavors that would eventually satisfy and attract more tea drinkers worldwide.


Assuntos
Cafeína/biossíntese , Camellia sinensis/química , Bebidas , Genômica/métodos , Folhas de Planta/genética , Folhas de Planta/metabolismo , Proteínas de Plantas/genética
10.
Oncotarget ; 8(26): 42116-42124, 2017 Jun 27.
Artigo em Inglês | MEDLINE | ID: mdl-28178669

RESUMO

By analyzing 4987 cancer transcriptomes from The Cancer Genome Atlas (TCGA), we identified that excision repair cross-complementation group 6 like (ERCC6L), a newly discovered DNA helicase, is highly expressed in 12 solid cancers. However, its role and mechanism in tumorigenesis are largely unknown. In this study, we found that ERCC6L silencing by small interring RNA (siRNA) or short hairpin RNA (shRNA) significantly inhibited the proliferation of breast (MCF-7, MDA-MB-231) and kidney cancer cells (786-0). Furthermore, ERCC6L silencing induced cell cycle arrest at G0/G1 phase without affecting apoptosis. We then performed RNA sequencing (RNA-seq) analysis after ERCC6L silencing and identified that RAB31 was markedly downregulated at both the transcriptional and translational levels. Its downstream protein, phosphorylated MAPK and CDK2 were also inhibited by ERCC6L silencing. The xenograft experiment showed that silencing of ERCC6L strikingly inhibited tumor growth from the 7th day after xenograft in nude mice. In addition, higher ERCC6L expression was found to be significantly associated with worse clinical survival in breast and kidney cancers. In conclusion, our results suggest that ERCC6L may stimulates cancer cell proliferation by promoting cell cycle through a way of RAB31-MAPK-CDK2, and it could be a potential biomarker for cancer prognosis and target for cancer treatment.


Assuntos
Neoplasias da Mama/genética , Neoplasias da Mama/mortalidade , DNA Helicases/genética , Neoplasias Renais/genética , Neoplasias Renais/mortalidade , Animais , Apoptose/genética , Neoplasias da Mama/metabolismo , Neoplasias da Mama/patologia , Pontos de Checagem do Ciclo Celular/genética , Linhagem Celular Tumoral , Proliferação de Células , Modelos Animais de Doenças , Progressão da Doença , Feminino , Técnicas de Silenciamento de Genes , Inativação Gênica , Xenoenxertos , Humanos , Neoplasias Renais/metabolismo , Neoplasias Renais/patologia , Masculino , Camundongos , Proteínas Quinases Ativadas por Mitógeno/genética , Proteínas Quinases Ativadas por Mitógeno/metabolismo , Prognóstico , Proteínas rab de Ligação ao GTP/genética , Proteínas rab de Ligação ao GTP/metabolismo
11.
Artigo em Inglês | MEDLINE | ID: mdl-27833660

RESUMO

BACKGROUND: Long noncoding RNAs (lncRNAs) are a class of ubiquitous noncoding RNAs and have been found to act as tumor suppressors or oncogenes, which dramatically altered our understanding of cancer. Naked mole rat (NMR, Heterocephalus glaber) is an exceptionally long-lived and cancer-resistant rodent; however, whether lncRNAs play roles in cancer resistance in this seductive species remains unknown. RESULTS: In this study, we developed a pipeline and identified a total of 4422 lncRNAs across the NMR genome based on 12 published transcriptomes. Systematic analysis revealed that NMR lncRNAs share many common characteristics with other vertebrate species, such as tissue specificity and low expression. BLASTN against with 1057 human cancer-related lncRNAs showed that only 5 NMR lncRNAs displayed homology, demonstrating the low sequence conservation between NMR lncRNAs and human cancer-related lncRNAs. Further correlation analysis of lncRNAs and protein-coding genes indicated that a total of 1295 lncRNAs were intensively coexpressed (r ≥ 0.9 or r ≤ -0.9, cP value ≤ 0.01) with potential tumor-suppressor genes in NMR, and 194 lncRNAs exhibited strong correlation (r ≥ 0.8 or r ≤ -0.8, cP value ≤ 0.01) with four high-molecular-mass hyaluronan related genes that were previously identified to play key roles in cancer resistance of NMR. CONCLUSION: In this study, we provide the first comprehensive genome-wide analysis of NMR lncRNAs and their possible associations with cancer resistance. Our results suggest that lncRNAs may have important effects on anticancer mechanism in NMR.


Assuntos
Resistência à Doença/genética , Ratos-Toupeira/genética , Neoplasias/genética , RNA Longo não Codificante/metabolismo , Animais , Bases de Dados Genéticas , Genoma , Humanos , Camundongos , Neoplasias/metabolismo , Neoplasias/patologia , RNA Longo não Codificante/genética , Ratos , Transcriptoma
12.
Neurobiol Aging ; 47: 218.e11-218.e18, 2016 11.
Artigo em Inglês | MEDLINE | ID: mdl-27600867

RESUMO

Reduced mitochondrial function is an important cause of aging and age-related diseases. We previously revealed a relatively higher level of mitochondrial DNA (mtDNA) content in centenarians. However, it is still unknown whether such an mtDNA content pattern of centenarians could be passed on to their offspring and how it was regulated. To address these issues, we recruited 60 longevity families consisting of 206 family members (cohort 1) and explored their mtDNA copy number. The results showed that the first generation of the offspring (F1 offspring) had a higher level of mtDNA copy number than their spouses (p < 0.05) independent of a gender effect. In addition, we found a positive association of mtDNA copy number in centenarians with that in F1 offspring (r = 0.54, p = 0.0008) but not with that in F1 spouses. These results were replicated in another independent cohort consisting of 153 subjects (cohort 2). RNA sequencing analysis suggests that the single-stranded DNA-binding protein 4 was significantly associated with mtDNA copy number and was highly expressed in centenarians as well as F1 offspring versus the F1 spouses, thus likely regulates the mtDNA copy number in the long-lived family members. In conclusion, our results suggest that the pattern of high mtDNA copy number is likely inheritable, which may act as a favorable factor to familial longevity through assuring adequate energy supply.


Assuntos
Variações do Número de Cópias de DNA/genética , DNA Mitocondrial/genética , Estudos de Associação Genética , Longevidade/genética , Idoso de 80 Anos ou mais , Proteínas de Ligação a DNA/genética , Metabolismo Energético/genética , Feminino , Humanos , Masculino
13.
Sci Rep ; 6: 30135, 2016 07 26.
Artigo em Inglês | MEDLINE | ID: mdl-27456469

RESUMO

Prokaryotes possess a simple genome transcription system that is different from that of eukaryotes. In chloroplasts (plastids), it is believed that the prokaryotic gene transcription features govern genome transcription. However, the polycistronic operon transcription model cannot account for all the chloroplast genome (plastome) transcription products at whole-genome level, especially regarding various RNA isoforms. By systematically analyzing transcriptomes of plastids of algae and higher plants, and cyanobacteria, we find that the entire plastome is transcribed in photosynthetic green plants, and that this pattern originated from prokaryotic cyanobacteria - ancestor of the chloroplast genomes that diverged about 1 billion years ago. We propose a multiple arrangement transcription model that multiple transcription initiations and terminations combine haphazardly to accomplish the genome transcription followed by subsequent RNA processing events, which explains the full chloroplast genome transcription phenomenon and numerous functional and/or aberrant pre-RNAs. Our findings indicate a complex prokaryotic genome regulation when processing primary transcripts.


Assuntos
Eucariotos/genética , Genoma de Cloroplastos , Fotossíntese , Transcrição Genética , Cianobactérias/genética , Modelos Genéticos , Plastídeos/genética , Edição de RNA , Reação em Cadeia da Polimerase em Tempo Real , Análise de Sequência de RNA
14.
Sci Rep ; 6: 21962, 2016 Feb 25.
Artigo em Inglês | MEDLINE | ID: mdl-26911903

RESUMO

Centenarians are a good healthy aging model. Interestingly, centenarians' offspring are prone to achieve longevity. Here we recruited 60 longevity families and investigated the blood biochemical indexes of family members to seek candidate factors associated with familial longevity. First, associations of blood indexes with age were tested. Second, associations of blood parameters in centenarians (CEN) with their first generation of offspring (F1) and F1 spouses (F1SP) were analyzed. Third, genes involved in regulating target factors were investigated. We found that total cholesterol (TC) and triglyceride (TG) increased with age (20-80 years), but decreased in CEN. Similarly, blood urea nitrogen (BUN) and blood creatinine (BCr) increased with age (20-80 years), but were maintained on a plateau in CEN. Importantly, we first revealed dual changes in blood pressure, i.e., decreased diastolic blood pressure but increased systolic blood pressure in CEN, which associated with altered CST3 expression. Genetic analysis revealed a significant association of blood uric acid (BUA) and BCr in CEN with F1 but not with F1SP, suggesting they may be heritable traits. Taken together, our results suggest serum lipids, kidney function and especially diastolic pressure rather than systolic pressure were improved in CEN or their offspring, suggesting these factors may play an important role in familial longevity.


Assuntos
Pressão Sanguínea/fisiologia , Rim/metabolismo , Lipídeos/sangue , Longevidade , Adulto , Idoso , Idoso de 80 Anos ou mais , Envelhecimento , Grupo com Ancestrais do Continente Asiático , Nitrogênio da Ureia Sanguínea , China , Colesterol/sangue , Creatinina/sangue , Cistatina C/metabolismo , Humanos , Testes de Função Renal , Metabolismo dos Lipídeos/genética , Masculino , Pessoa de Meia-Idade , Transcriptoma , Triglicerídeos/sangue , Ácido Úrico/sangue
15.
Artigo em Inglês | MEDLINE | ID: mdl-25103443

RESUMO

In this study, we report the complete mitochondrial genome sequence of brandt's bat, Myotis brandtii. The genome is found to be 17,470 bp in length and has a base composition of A (33.1%), G (13.6%), C (24.6%), and T (28.6%). Similar to other bats, it contains a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (D-loop). Most of the genes are encoded on H-strand, except for the eight tRNA and ND6 genes. All protein-coding genes start with an ATG codon except for ND2, ND3 and ND5, which initiate with ATC or ATA instead, and terminate with the typical stop codon (TAA/TAG) or a single T (T- -) or an unexpected codon of AGA. The complete mitochondrial genome sequence provided here would be useful for further phylogenetic analysis and population genetic studies in M. brandtii.


Assuntos
Quirópteros/genética , Genoma Mitocondrial , Mitocôndrias/genética , Animais , Composição de Bases , Ordem dos Genes , Tamanho do Genoma , Análise de Sequência de DNA/métodos
16.
Artigo em Inglês | MEDLINE | ID: mdl-24438258

RESUMO

In this study, we report the complete mitochondrial genome sequence of western painted turtle, Chrysemys picta bellii. The genome is found to be 16,875 bp in length and has a base composition of A (34.4%), G (13.0%), C (26.0%), and T (26.6%). Similar to other turtles, it contains a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (D-loop). Most of the genes are encoded on H-strand, except for the eight tRNA and ND6 genes. All protein-coding genes start with an ATN codon except for COX1 and ND4, which initiate with GTG instead, and terminate with the typical stop codon (TAA/TAG) or a single T (T-) or an unexpected codon of AGG. The complete mitochondrial genome sequence provided here would be useful for further phylogenetic analysis and conservation genetic studies in C. p. bellii.


Assuntos
Genoma Mitocondrial , Tartarugas/genética , Animais , Composição de Bases , Sequência de Bases , DNA Mitocondrial , Dados de Sequência Molecular , Filogenia , Análise de Sequência de DNA/veterinária
17.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(3): 1587-8, 2016 05.
Artigo em Inglês | MEDLINE | ID: mdl-25208182

RESUMO

In this study, we report the complete mitochondrial genome sequence of David's myotis, Myotis davidii. The genome is found to be 17,531 bp in length and has a base composition of A (33.8%), G (13.2%), C (23.2%), and T (29.8%). Similar to other bats, it contains a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (D-loop). Most of the genes are encoded on H-strand, except for the ND6 subunit gene and 8 tRNA genes. All protein-coding genes start with an ATG codon except for ND2, ND3 and ND5, which initiate with ATT or ATA instead, and terminate with the typical stop codon (TAA/TAG) or a single T (T-) or an unexpected codon of AGA. The complete mitochondrial genome sequence provided here would be useful for further phylogenetic analysis and population genetic studies in M. davidii.


Assuntos
Quirópteros/genética , Genoma Mitocondrial , Animais , Composição de Bases , Códon de Iniciação , Códon de Terminação , DNA Mitocondrial/química , DNA Mitocondrial/isolamento & purificação , DNA Mitocondrial/metabolismo , Fases de Leitura Aberta/genética , RNA Ribossômico/química , RNA Ribossômico/isolamento & purificação , RNA Ribossômico/metabolismo , RNA de Transferência/química , RNA de Transferência/isolamento & purificação , RNA de Transferência/metabolismo , Análise de Sequência de DNA
18.
Guang Pu Xue Yu Guang Pu Fen Xi ; 35(9): 2588-95, 2015 Sep.
Artigo em Chinês | MEDLINE | ID: mdl-26669173

RESUMO

In-situ experimental results on the elastic wave velocity of Earth materials at high pressure and high temperature in combination with data from seismic observation can help to inverse the chemical composition, state and migration of materials in Earth's interior, providing an important approach to explore information of deep earth. Applying the Brillouin scattering into the Diamond Anvil Cell (DAC) to obtain the in situ elastic wave velocities of minerals, is the important approach to investigate elastic properties of Earth's Interior. With the development of DAC technology, on the one hand, the high temperature and high pressure experimental environment to simulate different layers of the earth can be achieved; on the other hand, the optical properties of DAC made many kinds of optical analysis and test methods have been widely applied in this research field. In order to gain the elastic wave velocity under high temperature and high pressure, the accurate experimental pressure and heating temperature of the sample in the cavity should be measured and calibrated first, then the scattering signal needs to dealt with, using the Brillouin frequency shift to calculate the velocity in the sample. Combined with the lattice constants obtained from X ray technique, by a solid elastic theory, all the elastic parameters of minerals can be solved. In this paper, firstly, application of methods based on optical spectrum such as Brillouin and Raman scattering in elasticity study on materials in Earth's interior, and the basic principle and research progress of them in the velocity measurement, pressure and temperature calibration are described in detail. Secondly, principle and scope of application of two common methods of spectral pressure calibration (fluorescence and Raman spectral pressure standard) are analyzed, in addition with introduce of the application of two conventional means of temperature calibration (blackbody radiation and Raman temperature scale) in temperature determination. Lastly, geophysical applications of mineral elasticity are discussed on the basis of the recent research results derive from Brillouin scattering system of wave velocities for major minerals in Earth's lower mantle (perovskite, ferropericlase, etc.), and the future research work is inspected.

19.
BMC Genomics ; 16: 298, 2015 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-25881092

RESUMO

BACKGROUND: Camellia taliensis is one of the most important wild relatives of cultivated tea tree, C. sinensis. The species extensively occupies mountainous habitats representing a wide-range abiotic tolerance and biotic resistance and thus harbors valuable gene resources that may greatly benefit genetic improvement of cultivated tea tree. However, owning to a large genome size of ~3 Gb and structurally complex genome, there are fairly limited genetic information and particularly few genomic resources publicly available for this species. To better understand the key pathways determining tea flavor and enhance tea tree breeding programs, we performed a high-throughput transcriptome sequencing for C. taliensis. RESULTS: In this study, approximate 241.5 million high-quality paired-end reads, accounting for ~24 Gb of sequence data, were generated from tender shoots, young leaves, flower buds and flowers using Illumina HiSeq 2000 platform. De novo assembly with further processing and filtering yielded a set of 67,923 transcripts with an average length of 685 bp and an N50 of 995 bp. Based on sequence similarity searches against public databases, a total of 39,475 transcripts were annotated with gene descriptions, conserved protein domains or gene ontology (GO) terms. Candidate genes for major metabolic pathways involved in tea quality were identified and experimentally validated using RT-qPCR. Further gene expression profiles showed that they are differentially regulated at different developmental stages. To gain insights into the evolution of these genes, we aligned them to the previously cloned orthologous genes in C. sinensis, and found that considerable nucleotide variation within several genes involved in important secondary metabolic biosynthesis pathways, of which flavone synthase II gene (FNSII) is the most variable between these two species. Moreover, comparative analyses revealed that C. taliensis shows a remarkable expansion of LEA genes, compared to C. sinensis, which might contribute to the observed stronger stress resistance of C. taliensis. CONCLUSION: We reported the first large-coverage transcriptome datasets for C. taliensis using the next-generation sequencing technology. Such comprehensive EST datasets provide an unprecedented opportunity for identifying genes involved in several major metabolic pathways and will accelerate functional genomic studies and genetic improvement efforts of tea trees in the future.


Assuntos
Redes e Vias Metabólicas/genética , Chá/genética , Transcriptoma/genética , Bases de Dados Genéticas , Flores/genética , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Análise de Sequência de DNA , Chá/crescimento & desenvolvimento
20.
Front Plant Sci ; 6: 1171, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26779212

RESUMO

Simple sequence repeats (SSRs), also known as microsatellites, are ubiquitous short tandem duplications commonly found in genomes and/or transcriptomes of diverse organisms. They represent one of the most powerful molecular markers for genetic analysis and breeding programs because of their high mutation rate and neutral evolution. However, traditionally experimental screening of the SSR polymorphic status and their subsequent applicability to genetic studies are extremely labor-intensive and time-consuming. Thankfully, the recently decreased costs of next generation sequencing and increasing availability of large genome and/or transcriptome sequences have provided an excellent opportunity and sources for large-scale mining this type of molecular markers. However, current tools are limited. Thus we here developed a new pipeline, CandiSSR, to identify candidate polymorphic SSRs (PolySSRs) based on the multiple assembled sequences. The pipeline allows users to identify putative PolySSRs not only from the transcriptome datasets but also from multiple assembled genome sequences. In addition, two confidence metrics including standard deviation and missing rate of the SSR repetitions are provided to systematically assess the feasibility of the detected PolySSRs for subsequent application to genetic characterization. Meanwhile, primer pairs for each identified PolySSR are also automatically designed and further evaluated by the global sequence similarities of the primer-binding region, ensuring the successful rate of the marker development. Screening rice genomes with CandiSSR and subsequent experimental validation showed an accuracy rate of over 90%. Besides, the application of CandiSSR has successfully identified a large number of PolySSRs in the Arabidopsis genomes and Camellia transcriptomes. CandiSSR and the PolySSR marker sources are publicly available at: http://www.plantkingdomgdb.com/CandiSSR/index.html.

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