RESUMO
We attempted to identify significant pathway cross-talk in rheumatoid arthritis (RA) by the Monte Carlo cross-validation (MCCV) method. We therefore obtained and preprocessed the gene expression profile of RA. MCCV involves identifying differentially expressed genes (DEGs), identifying differential pathways (DPs), calculating the discriminating score (DS) of the pathway cross-talk, and random forest (RF) classification. We carried out 50 bootstrap iterations of MCCV to identify the key instances of pathway cross-talk involved in RA. We identified a total of 17 significant DEGs and 15 significant DPs by comparing RA samples and normal controls. We found the most significant difference between RA and the normal controls in the eIF4 and p70S6K signaling regulation pathway. Furthermore, we identified 10 instances of pathway cross-talk with the best classification performance for RA and normal controls, using the RF classification model. All of the top 10 pathway pairs involved cross-talk with eIF4 and p70S6K signaling regulation, and the other 10 pathways were immune-related. By MCCV, we identified one critical DP and 10 significant instances of pathway cross-talk in RA. We propose that the eIF4 and p70S6K signaling regulation pathway and the other significant instances of pathway cross-talk play key roles in the occurrence and development of RA, and are potential predictive and prognostic markers for RA.
Assuntos
Artrite Reumatoide/genética , Perfilação da Expressão Gênica/métodos , Artrite Reumatoide/metabolismo , Humanos , Modelos Genéticos , Método de Monte Carlo , Transdução de Sinais , TranscriptomaRESUMO
Suyunuo is a valuable glutinous rice variety cultivated mainly in the Lake Taihu area of China. Historically, Suyunuo was presented to emperors as a tribute, and, still today, enjoys a great reputation in China. This study aimed to develop a unique, specific molecular marker for the identification of Suyunuo rice. Polymerase chain reaction (PCR) amplification of inter-simple sequence repeat (ISSR) molecular markers was performed on Suyunuo and 11 other glutinous rice varieties that are mainly cultivated in the Yangtze River Delta region. A Suyunuo-specific band was detected in the PCR products generated from primer ISSR-807. A sequence characterized amplified region (SCAR) primer pair targeting a Suyunuo-specific band was subsequently designed. The SCAR primers amplified a target band in all individuals of Suyunuo and in four glutinous indica varieties, whereas no bands were found in the seven glutinous japonica varieties. Subsequently, sequences amplified by the SCAR primer pair were analyzed to facilitate the design of Suyunuo allele-specific primers. The allele-specific primer pair produced target bands in all individuals of Suyunuo rice but no bands in individuals of any of the other 11 rice varieties. This study provides a theoretical guideline for rice germplasm identification and innovation of other valuable rice landraces.
Assuntos
Alelos , Repetições de Microssatélites/genética , Oryza/genética , Reação em Cadeia da Polimerase/métodos , Sequência de Bases , Primers do DNA/metabolismo , Eletroforese em Gel de Ágar , Marcadores Genéticos , Reprodutibilidade dos Testes , Alinhamento de SequênciaRESUMO
Knowledge of genetic diversity is important to assist breeders in the selection of parental materials and in the design of breeding programs. In this study, we genotyped 348 inbred tomato lines, representing vintage and contemporary fresh-market varieties, by using 52 single nucleotide polymorphisms (SNPs); 45 of these were found to be polymorphic. The average minor allele frequency and unbiased expected heterozygosity were 0.315 and 0.356, respectively. Population structure analysis revealed that contemporary germplasm could be distinctly divided into six subpopulations representing three market classes and breeding programs (pink, green, and red). Vintage germplasm could be separated into at least two subpopulations, and more admixtures were found in vintage lines than in contemporary lines. These findings indicate that contemporary inbred lines are more diversified than vintage inbred lines. AMOVA of vintage and contemporary lines was performed. A significant difference was found (P < 0.01), which explained 17.4% of the total genetic variance. Subsequently, we constructed a core collection using 45 polymorphic SNP markers. The data showed that all alleles were captured by only 2% of lines, indicating that more alleles, as well as rare alleles, could enable more variation to be captured in the core collection. These data allow us to discard redundant inbred tomato lines and to select elite inbred lines, which will accelerate the breeding process.
Assuntos
Polimorfismo de Nucleotídeo Único , Sementes/genética , Solanum lycopersicum/genética , Frequência do Gene , Genes de Plantas , Estudos de Associação Genética , Marcadores Genéticos , Genótipo , Melhoramento Vegetal , Análise de Sequência de DNARESUMO
Colocasia esculenta cv. Xinmaoyu is an eddoe-type taro cultivar local to Taicang, Jiangsu Province, China; it is characterized by its pure flavor, glutinous texture, and high nutritional value. Due to its excellent qualities, the Trademark Office of the State Administration for Industry and Commerce of the People's Republic of China awarded Xinmaoyu, a geographical indication certification in 2014. Therefore, there is an urgent need to develop an efficient molecular marker for the specific identification of this cultivar, which would greatly facilitate the conservation and utilization of this unique germplasm resource. In the present study, amplifying the psbE-petL fragment from two dasheen-type and seven eddoe-type taro cultivars revealed three conserved insertions/deletions among sequences from the two taro types. Based on these sequence differences, a pair of site-specific primers was designed targeting the psbE-petL sequence from the dasheen-type taro, which specifically amplified a DNA band in all individuals from cultivars of this type, but not in those from the seven eddoe-type cultivars. To discriminate Xinmaoyu from the other eddoe-type taro cultivars, a pair of simple sequence repeat-sequence characterized amplified region (SSR-SCAR) primers was further developed to specifically amplify a DNA band from all Xinmaoyu individuals, but not from individuals of other eddoe-type taro cultivars. In conclusion, through a two-step-screening procedure using psbE-petL and SSR-SCAR markers, we developed a pair of primers that could specifically discriminate Xinmaoyu from nine taro cultivars commonly cultivated in Jiangsu Province and Fujian Province.
Assuntos
Colocasia/genética , Marcadores Genéticos , Repetições de Microssatélites , Colocasia/classificação , HumanosRESUMO
Non-heading Chinese cabbage [Brassica rapa var. chinensis (Linnaeus) Kitamura] is a popular vegetable and is also used as a medicinal plant in traditional Chinese medicine. Fragrant Bok Choy is a unique accession of non-heading Chinese cabbage and a product of geographic indication certified by the Ministry of Agriculture of China, which is noted for its rich aromatic flavor. However, transitional and overlapping morphological traits can make it difficult to distinguish this accession from other non-heading Chinese cabbages. This study aimed to develop a molecular method for efficient identification of Fragrant Bok Choy. Genetic diversity analysis, based on inter-simple sequence repeat molecular markers, was conducted for 11 non-heading Chinese cabbage accessions grown in the Yangtze River Delta region. Genetic similarity coefficients between the 11 accessions ranged from 0.5455 to 0.8961, and the genetic distance ranged from 0.0755 to 0.4475. Cluster analysis divided the 11 accessions into two major groups. The primer ISSR-840 amplified a fragment specific for Fragrant Bok Choy. A pair of specific sequence-characterized amplified region (SCAR) primers based on this fragment amplified a target band in Fragrant Bok Choy individuals, but no band was detected in individuals of other accessions. In conclusion, this study has developed an efficient strategy for authentication of Fragrant Bok Choy. The SCAR marker described here will facilitate the conservation and utilization of this unique non-heading Chinese cabbage germplasm resource.
Assuntos
Brassica rapa/genética , Variação Genética , Repetições de Microssatélites/genética , Brassica rapa/crescimento & desenvolvimento , China , Marcadores Genéticos , Folhas de Planta/genética , Folhas de Planta/crescimento & desenvolvimentoRESUMO
Brassicaceae is a large plant family of special interest; it includes many economically important crops, herbs, and ornamentals, as well as model organisms. The taxonomy of the Brassicaceae has long been controversial because of the poorly delimited generic boundaries and artificially circumscribed tribes. Despite great effort to delimitate species and reconstruct the phylogeny of Brassicaceae, little research has been carried out to investigate the applicability and effectiveness of different DNA regions as barcodes - a recent aid for taxonomic identification - to identify economically important species in Brassicaceae. In this study, we evaluated the feasibility of five intensively recommended regions [rbcL, matK, trnH-psbA, internal transcribed spacer (ITS), ITS2] as candidate DNA barcodes to discriminate economic species of Brassicaceae in China and try to establish a new digital identification method for economic plants of Brassicaceae. All sequences of 58 samples from 27 economic species (Brassicaceae) in China were assessed in the success rates of PCR amplifications, intra- and inter-specific divergence, DNA barcoding gaps, and efficiency of identification. Compared with other markers, ITS showed superiority in species discrimination with an accurate identification of 67.2% at the species level. Consequently, as one of the most popular phylogenetic markers, our study indicated that ITS was a powerful but not perfect barcode for Brassicaceae identification. We further discuss the discrimination power of different loci due to inheritance pattern, polyploidization and hybridization in species-specific evolution. Further screening of other nuclear genes related to species isolation as plant barcode candidates is also proposed.
Assuntos
Brassicaceae/genética , Código de Barras de DNA Taxonômico/métodos , Variação Genética , Brassicaceae/classificação , China , DNA de Plantas/química , DNA de Plantas/genética , DNA Espaçador Ribossômico/química , DNA Espaçador Ribossômico/genética , Loci Gênicos/genética , Marcadores Genéticos/genética , Filogenia , Proteínas de Plantas/genética , Análise de Sequência de DNA , Especificidade da EspécieRESUMO
We evaluated the effects of down-regulated heme oxygenase (HO)-1 expression on the proliferation of the acute myelocytic leukemia Kasumi-1 cell line by using the HO-1 inhibitor zinc protoporphyrin IX (ZnPPIX) in combination with daunorubicin (DNR), and evaluated the mechanism. The proliferation rates of cells treated with 10 mg/mL DNR and 10 mM ZnPPIX individually or in combination for different time periods were detected using the MTT assay. The apoptotic outcomes of the blank control, ZnPPIX, DNR, and ZnPPIX groups in combination with the DNR group were detected by flow cytometry. The expression of HO-1, activating transcription factor 4, CCAAT-enhancer-binding protein homologous protein, and inositol-requiring enzyme-α mRNA and proteins were detected by fluorescent quantitative real-time polymerase chain reaction and western blotting, respectively. Combined administration inhibited the cells most potently and time-dependently, decreased the expression of HO-1, and significantly increased the expression of activating transcription factor 4, CCAAT-enhancer-binding protein homologous protein, and inositol-requiring enzyme-α expression levels. The cell apoptotic rates in the blank control, DNR, ZnPPIX, and combined administration groups were 8.32 ± 0.53, 39.16 ± 1.46, 10.46 ± 0.88, and 56.26 ± 2.24%, respectively. Inhibiting HO-1 expression can enhance the damaging effects of DNR on Kasumi-1 cells, providing experimental evidence for the improvement of therapeutic effects on acute myelocytic leukemia in clinical practice.
Assuntos
Fator 4 Ativador da Transcrição/biossíntese , Endorribonucleases/biossíntese , Heme Oxigenase-1/biossíntese , Leucemia Mieloide Aguda/genética , Proteínas Serina-Treonina Quinases/biossíntese , Fator de Transcrição CHOP/biossíntese , Fator 4 Ativador da Transcrição/genética , Apoptose/efeitos dos fármacos , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Endorribonucleases/genética , Inibidores Enzimáticos/administração & dosagem , Regulação Leucêmica da Expressão Gênica/efeitos dos fármacos , Heme Oxigenase-1/antagonistas & inibidores , Heme Oxigenase-1/genética , Humanos , Leucemia Mieloide Aguda/tratamento farmacológico , Leucemia Mieloide Aguda/patologia , Proteínas Serina-Treonina Quinases/genética , RNA Mensageiro/biossíntese , Transdução de Sinais/efeitos dos fármacos , Fator de Transcrição CHOP/genéticaRESUMO
Heterosis has been widely used in crop breeding and production. However, a shortage of genes known to function in heterosis significantly limits our understanding of the molecular basis underlying heterosis. Here, we report 740 differentially expressed genes (DEGs) in the leaves of the hybrid millet Zhang No.5 and its parents at the grain filling stage determined using Solexa Illumina digital gene expression. Of the 740 DEGs, 546 were from the hybrid and its parents and most were up-regulated in the hybrid. Particularly, a large number of DEGs related to starch and carbohydrate metabolism and 2 DEGs encoding chlorophyll a/b binding proteins were up-regulated in hybrid millet. Moreover, all DEGs were enriched in the biological process and molecular function, and no DEGs were found to be enriched in the cellular component of GO terms. Pathway enrichment using KEGG showed that several DEGs were enriched in the circadian rhythm pathway. Further analysis revealed that the altered circadian rhythm, which mediates photosynthesis and carbohydrate accumulation, may play an important role in heterosis of the hybrid millet.
Assuntos
Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Hibridização Genética , Milhetes/genética , Sementes/genética , Metabolismo dos Carboidratos/genética , Ritmo Circadiano/genética , Ontologia Genética , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Fotossíntese/genética , Reação em Cadeia da Polimerase em Tempo RealRESUMO
Ganoderma mushroom is one of the most prescribed traditional medicines and has been used for centuries, particularly in China, Japan, Korea, and other Asian countries. In this study, different strains of Ganoderma spp and the genetic relationships of the closely related strains were identified and investigated based on the V4-V6 region of mitochondrial small subunit ribosomal DNA of the Ganoderma species. The sizes of the mitochondrial ribosomal DNA regions from different Ganoderma species showed 2 types of sequences, 2.0 or 0.5 kb. A phylogenetic tree was constructed, which revealed a high level of genetic diversity in Ganoderma species. Ganoderma lucidum G05 and G. eupense G09 strains were clustered into a G. resinaceum group. Ganoderma spp G29 and G22 strains were clustered into a G. lucidum group. However, Ganoderma spp G19, G20, and G21 strains were clustered into a single group, the G. lucidum AF214475, G. sinense, G. strum G17, G. strum G36, and G. sinense G10 strains contained an intron and were clustered into other groups.
Assuntos
DNA Mitocondrial/genética , DNA Ribossômico/genética , Ganoderma/genética , Variação Genética , China , Ganoderma/classificação , Humanos , Japão , Medicina Tradicional Chinesa , Filogenia , República da CoreiaRESUMO
Camellia ptilophylla, or cocoa tea, is naturally decaffeinated and its predominant catechins and purine alkaloids are trans-catechins and theobromine Regular tea [Camellia sinensis (L.) O. Ktze.] is evolutionarily close to cocoa tea and produces cis-catechins and caffeine. Here, the transcriptome of C. ptilophylla was sequenced using the 101-bp paired-end technique. The quality of the raw data was assessed to yield 70,227,953 cleaned reads totaling 7.09 Gbp, which were assembled de novo into 56,695 unique transcripts and then clustered into 44,749 unigenes. In catechin biosynthesis, leucoanthocyanidin reductase (LAR) catalyzes the transition of leucoanthocyanidin to trans-catechins, while anthocyanidin synthase (ANS) and anthocyanidin reductase (ANR) catalyze cis-catechin production. Our data demonstrate that two LAR genes (CpLAR1 and CpLAR2) by C. ptilophylla may be advantageous due to the combined effects of this quantitative trait, permitting increased leucoanthocyanidin consumption for the synthesis of trans-catechins. In contrast, the only ANS gene observed in C. sinensis (CsANS) shared high identity (99.2%) to one homolog from C. ptilophylla (CpANS1), but lower identity (~80%) to another (CpANS2). We hypothesized that the diverged CpANS2 might have lost its ability to synthesize cis-catechins. C. ptilophylla and C. sinensis each contain two copies of ANR, which share high identity and may share the same function. Transcriptomic sequencing captured two N-methyl nucleosidase genes named NMT1 and NMT2. NMT2 was highly identical to three orthologous genes TCS2, PCS2, and ICS2, which did not undergo methylation in vitro; in contrast, NMT1 was less identical to TCS, PCS and ICS, indicating that NMT1 may undergo neofunctionalization.
Assuntos
Camellia/genética , Regulação da Expressão Gênica de Plantas , N-Glicosil Hidrolases/genética , Oxirredutases/genética , Oxigenases/genética , Proteínas de Plantas/genética , Transcriptoma , Antocianinas/biossíntese , Cafeína/biossíntese , Camellia/classificação , Camellia/metabolismo , Camellia sinensis/classificação , Camellia sinensis/genética , Camellia sinensis/metabolismo , Catequina/biossíntese , Flavonoides/biossíntese , Sequenciamento de Nucleotídeos em Larga Escala , Isoenzimas/genética , Isoenzimas/metabolismo , N-Glicosil Hidrolases/metabolismo , Oxirredutases/metabolismo , Oxigenases/metabolismo , Filogenia , Proteínas de Plantas/metabolismo , Característica Quantitativa Herdável , Teobromina/biossínteseRESUMO
A genome-wide association study revealed that a single nucleotide polymorphism, CLPTM1L - rs401681 (G>A), located at the 5p15.33 locus was significantly associated with increased risk of various cancers; however, its association with lung cancer is currently inconclusive. In order to explore the relationship between this polymorphism and lung cancer risk more precisely, we performed a meta-analysis of eight eligible studies involving 9935 cases and 11,261 controls. The pooled odds ratio (OR) and the 95% confidence interval (CI) were calculated using a fixed- or random-effect models. Results indicated that this polymorphism was significantly associated with lung cancer risk in all genetic models (GA vs GG: OR = 0.88, 95%CI = 0.83-0.94; AA vs GG: OR = 0.81, 95%CI = 0.70-0.93; AA/GA vs GG: OR = 0.86, 95%CI = 0.81-0.91; AA vs GA/GG: OR = 0.86, 95%CI = 0.76-0.99). An analysis stratified by ethnicity and source of controls revealed a significantly decreased risk among European groups and population-based studies in all genetic models, and among Asian populations only in the dominant model comparison. Additionally, in a subgroup analysis by histology type, the CLPTM1L rs401681 polymorphism was found to significantly decrease the risks of both adenocarcinoma and squamous cell carcinoma of the lung in all genetic models. In conclusion, our study indicated that the CLPTM1L - rs401681 (G>A) polymorphism was significantly associated with decreased lung cancer risk, especially among European populations. Due to some minor limitations, our findings should be confirmed in further studies.
Assuntos
Predisposição Genética para Doença , Neoplasias Pulmonares/genética , Proteínas de Membrana/genética , Proteínas de Neoplasias/genética , Polimorfismo de Nucleotídeo Único , Alelos , Estudos de Casos e Controles , Genótipo , Humanos , Neoplasias Pulmonares/epidemiologia , Razão de Chances , Viés de Publicação , RiscoRESUMO
Osteoarthritis is the most common form of arthritis among elderly adults. Herein, we performed protein-protein interaction (PPI) and miRNA network analysis to evaluate the global correlation between miRNA regulation and the PPI network in human osteoarthritis. Our results showed that desmoplakin (DSP), cystatin A (CSTA), calmodulin 1, tyrosine kinase endothelial, insulin-like growth factor 1 (IGF-1), IGF-binding protein 7 (IGFBP7), syndecan 1 (SDC1), ephrin type-A receptor 4, and PDZ and LIM domain protein 1 were associated with osteoarthritis. Among these proteins, DSP and CSTA interaction and IGF-1, IGFBP7 and SDC1 interaction were observed in our PPI network. Furthermore, these potential target proteins were also linked with individual miRNA in the network. Our findings shed light on the PPIs and mechanisms by which miRNA may regulate the protein interaction network in osteoarthritis, which might provide theoretical support for further studies aimed at discovering new therapeutic strategies.
Assuntos
MicroRNAs/genética , Osteoartrite/genética , Osteoartrite/metabolismo , Mapas de Interação de Proteínas , Cistatina A/metabolismo , Desmoplaquinas/metabolismo , Redes Reguladoras de Genes , Humanos , Proteínas de Ligação a Fator de Crescimento Semelhante a Insulina/metabolismo , Fator de Crescimento Insulin-Like I/metabolismo , Meniscos Tibiais/metabolismo , Meniscos Tibiais/patologia , Modelos Biológicos , Modelos Genéticos , Ligação Proteica , Mapeamento de Interação de Proteínas , Transdução de Sinais/genética , Sindecana-1/metabolismoRESUMO
In order to make a comprehensive assessment of the potential association between two genetic variants in the IL-10 gene promoter, -1082 A>G (rs1800896) and -592 C>A (rs1800872), and colorectal cancer (CRC) risk, we conduced a meta-analysis of seven epidemiological studies, which included 1469 colorectal cancer cases and 2566 controls. Neither of the two polymorphisms had any association with increased CRC risk in overall population [for rs1800896: odds ratio (OR) = 0.90, 95% confidence interval (95%CI) = 0.76-1.06 in the dominant model and for rs1800872: OR = 1.06, 95%CI = 0.91-1.23 in the dominant model]. In subgroup analysis of the rs1800896 polymorphism, the results did not change when the analyses were restricted to individual studies, or those fulfilling Hardy-Weinberg equilibrium, or according to the source of controls. For rs1800872, however, when stratifying by the source of controls, the A allele had a significant increased risk of CRC among studies with population-based controls in the codominant model (AC vs CC: OR = 1.30, 95%CI = 1.04-1.63) and dominant model (AA/AC vs CC: OR = 1.25, 95% CI = 1.01-1.55). Based on this meta-analysis, we conclude that the IL-10 rs1800872 polymorphism could be a risk factor for CRC development among European populations. However, we found no association between the IL-10 rs1800896 polymorphism and CRC risk. Further studies, either with larger sample size or involving other SNPs and haplotypes of the IL-10 gene, are necessary to clarify the contribution of IL-10 genetic variations in colorectal carcinogenesis.