Global analysis of differential expression in Coffea arabica seeds during the processing and drying.

Coffee is one of the most important agricultural commodities and ensures the livelihood of more than 80 million people worldwide. The mode of coffee processing, whether wet or dry, determines the flavor characteristic and also the seed quality. Novel, high-throughput, deep- sequencing technologies are making an impact on genomic research by providing new strategies to analyze the functional complexity of transcriptomes. The RNA-Seq approach produces millions of short cDNA reads that are mapped to a reference genome to obtain a genome-scale transcriptional map, which consists of the transcriptional structure and the expression level for each gene. In this study we applied Illumina sequencing technology and the Venn diagram analysis for differential expression. Coffee seeds were processed by three different methods, dry, semi-dry or wet, and were dried under shade or dryer conditions. The samples were used to prepare a cDNA library for sequence analysis via Illumina (HiSeq 2000). After removal of low-quality reads, a total of 125,829,579 high-quality 50 bp reads were identified. The reads were assembled using Trinity program using default parameters. It was compared our data against ESTs Brazilian Coffee Genome data and Coffee Colombian data. As can be seen in the Venn diagram representation, we ́ve got more blast in ESTs Brazilian Coffee Genome data than in Coffee Colombian data, indicating an alignment of 20,509 common sequences between ESTs Brazilian Coffee Genome and ?Assembly de Novo? sequence (our data)

Efficiency of coffee seeds rna extraction protoco using rna integrity number analysis.

Coffee is one of the most important agricultural products in the world market. The mode of coffee processing, whether wet or dry, determines the flavor characteristic and also the seed quality. Quality RNA isolation is a mandatory requirement for studies of gene expression, including reverse transcriptase (RT), real-time quantitative PCR (RT-qPCR), construction of cDNA libraries, or microarray analyses. Due to the presence of secondary metabolites, polysaccharides, and polyphenols, standardization of a quality RNA extraction for different coffee plant tissue is very difficult. Also, getting high-quality RNA may be complicated because of RNA susceptibility to RNase degradation

Differential expression in Coffea arabica seeds during the processing and drying.

Coffee is one of the most important agricultural products in the world market. The mode of coffee processing, whether wet or dry, determines the characteristic flavor and also the seed quality. In recent years, high-throughput RNA-sequencing (RNA-Seq) has emerged as a powerful and cost-efficient tool for transcriptome analysis. RNA-Seq has proven useful for the detection of gene expression, the discovery of novel transcripts, and the identification of differentially expressed genes. In this study, we applied Illumina sequencing technology and the Heat Map analysis for differential expression. Coffee seeds were processed by three different methods, dry, semi-dry or wet, and were dried under shade or dryer conditions. The samples were used to prepare a cDNA library for sequence analysis via Illumina (HiSeq 2000). After removal of low-quality reads, a total of 125,829,579 high-quality 50 bp reads were identified. As can be seen in the Heat Map graphic representation, semi-dry/dryer methods are separated from wet/dyer methods, with high differential expression. This representation indicates they have much differential expression in different metabolic pathways. However, semi-dry/shade and wet/shade have similar differential expression. These results provide information on how the processing and drying methods influences gene expression, and suggest that that more detailed analyzes in metabolic pathway studies are required

Regulatory modules controlling maize inflorescence architecture

Genetic control of branching is a primary determinant of yield, regulating seed number and harvesting ability, yet little is known about the molecular networks that shape grain-bearing inflorescences of cereal crops. Here, we used the maize (Zea mays) inflorescence to investigate gene networks that modulate determinacy, specifically the decision to allow branch growth. We characterized developmental transitions by associating spatiotemporal expression profiles with morphological changes resulting from genetic perturbations that disrupt steps in a pathway controlling branching. Developmental dynamics of genes targeted in vivo by the transcription factor RAMOSA1, a key regulator of determinacy, revealed potential mechanisms for repressing branches in distinct stem cell populations, including interactions with KNOTTED1, a master regulator of stem cell maintenance. Our results uncover discrete developmental modules that function in determining grass-specific morphology and provide a basis for targeted crop improvement and translation to other cereal crops with comparable inflorescence architectures

Tomato floral induction and flower development are orchestrated by the interplay between gibberellin and two unrelated microRNA-controlled modules

[EN] Age-regulated microRNA156 (miR156) and targets similarly control the competence to flower in diverse species. By contrast, the diterpene hormone gibberellin (GA) and the microRNA319-regulated TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) transcription factors promote flowering in the facultative long-day Arabidopsis thaliana, but suppress it in the day-neutral tomato (Solanum lycopersicum). We combined genetic and molecular studies and described a new interplay between GA and two unrelated miRNA-associated pathways that modulates tomato transition to flowering. Tomato PROCERA/DELLA activity is required to promote flowering along with the miR156-targeted SQUAMOSA PROMOTER BINDING-LIKE (SPL/SBP) transcription factors by activating SINGLE FLOWER TRUSS (SFT) in the leaves and the MADS-Boxgene APETALA1(AP1)/MC at the shoot apex. Conversely, miR319-targeted LANCEOLATE represses floral transition by increasing GA concentrations and inactivating SFT in the leaves and AP1/MC at the shoot apex. Importantly, the combination of high GA concentrations/responses with the loss of SPL/SPB function impaired canonical meristem maturation and flower initiation in tomato. Our results reveal a cooperative regulation of tomato floral induction and flower development, integrating age cues (miR156 module) with GA responses and miR319-controlled pathways. Importantly, this study contributes to elucidate the mechanisms underlying the effects of GA in controlling flowering time in a day-neutral species.We thank Dr C. Schommer for kindly providing tcp4-soj8/+ seeds, and Carlos Rojas for Arabidopsis flowering time analyses. This work was supported by FAPESP (grant no. 15/17892-7 and fellowships nos 15/23826-7 and 13/16949-0). The authors declare no conflict of interest.Silva, G.; Silva, E.; Correa, J.; Vicente, M.; Jiang, N.; Notini, M.; Junior, A.... (2018). 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Dickkopf-1 (Dkk-1) in plasma and synovial fluid is inversely correlated with radiographic severity of knee osteoarthritis patients

<p>Abstract</p> <p>Background</p> <p>Osteoarthritis (OA) is a common degenerative joint disease causing pain, stiffness, reduced motion, swelling, crepitus, and disability. Dickkopf-1 (Dkk-1) is a critical mediator of osteoblastogenesis and regulates the joint remodeling. The aim of this study was to examine plasma and synovial fluid Dkk-1 levels of patients with primary knee OA and to investigate their relationship with disease severity.</p> <p>Methods</p> <p>Thirty-five patients aged 55-83 years with knee OA and 15 healthy individuals were recruited into this study. Disease severity was determined using weight-bearing anteroposterior radiographs of the affected knee. The radiological grading of OA in the knee was performed according to the Kellgren-Lawrence grading system. Dkk-1 levels in both plasma and synovial fluid were evaluated using enzyme-linked immunosorbent assay.</p> <p>Results</p> <p>The average concentration of circulating Dkk-1 in the knee OA patients was remarkably lower than that of healthy controls (396.0 ± 258.8, 95%CI 307.1-484.9 vs 2348.8 ± 2051.5, 95%CI 1164.3-3533.3 pg/ml, p < 0.0001). Dkk-1 levels in synovial fluid were significantly lower than in paired plasma samples (58.6 ± 31.8, 95%CI 47.7-69.6 vs 396.0 ± 258.8, 95%CI 307.1-484.9 pg/ml, p < 0.001). Furthermore, both plasma and synovial fluid Dkk-1 levels were inversely correlated with radiographic severity (r = -0.78, p < 0.001 and r = -0.42, p = 0.01, respectively). Plasma Dkk-1 levels were also significantly correlated with synovial fluid Dkk-1 levels (r = 0.72, p < 0.001).</p> <p>Conclusions</p> <p>Dkk-1 levels in plasma and synovial fluid are inversely related to the severity of joint damage in knee OA. Dkk-1 could serve as a biochemical marker for determining disease severity and might play a potential role in the pathogenesis of the degenerative process of OA.</p

Light-induced vegetative anthocyanin pigmentation in Petunia

The Lc petunia system, which displays enhanced, light-induced vegetative pigmentation, was used to investigate how high light affects anthocyanin biosynthesis, and to assess the effects of anthocyanin pigmentation upon photosynthesis. Lc petunia plants displayed intense purple anthocyanin pigmentation throughout the leaves and stems when grown under high-light conditions, yet remain acyanic when grown under shade conditions. The coloured phenotypes matched with an accumulation of anthocyanins and flavonols, as well as the activation of the early and late flavonoid biosynthetic genes required for flavonol and anthocyanin production. Pigmentation in Lc petunia only occurred under conditions which normally induce a modest amount of anthocyanin to accumulate in wild-type Mitchell petunia [Petunia axillaris×(Petunia axillaris×Petunia hybrida cv. ‘Rose of Heaven’)]. Anthocyanin pigmentation in Lc petunia leaves appears to screen underlying photosynthetic tissues, increasing light saturation and light compensation points, without reducing the maximal photosynthetic assimilation rate (Amax). In the Lc petunia system, where the bHLH factor Leaf colour is constitutively expressed, expression of the bHLH (Lc) and WD40 (An11) components of the anthocyanin regulatory system were not limited, suggesting that the high-light-induced anthocyanin pigmentation is regulated by endogenous MYB transcription factors

A MYB/ZML complex regulates wound-induced lignin genes in maize

Lignin is an essential polymer in vascular plants that plays key structural roles in vessels and fibers. Lignification is induced by external inputs such as wounding, but the molecular mechanisms that link this stress to lignification remain largely unknown. In this work, we provide evidence that three maize (Zea mays) lignin repressors, MYB11, MYB31, and MYB42, participate in wound-induced lignification by interacting with ZML2, a protein belonging to the TIFY family. We determined that the three R2R3-MYB factors and ZML2 bind in vivo to AC-rich and GAT(A/C) cis-elements, respectively, present in a set of lignin genes. In particular, we show that MYB11 and ZML2 bind simultaneously to the AC-rich and GAT(A/C) cis-elements present in the promoter of the caffeic acid O-methyl transferase (comt) gene. We show that, like the R2R3-MYB factors, ZML2 also acts as a transcriptional repressor. We found that upon wounding and methyl jasmonate treatments, MYB11 and ZML2 proteins are degraded and comt transcription is induced. Based on these results, we propose a molecular regulatory mechanism involving a MYB/ZML complex in which wound-induced lignification can be achieved by the derepression of a set of lignin genes.Research in D.C.-R.'s laboratory was supported by a grant from the Spanish Ministry of Science and Education (AGL2011-30545-C02-01), the “Xarxa de Referència de Biotecnologia” (XarBa) from the Autonomous Government of Catalonia, the CONSOLIDER-INGENIO program (CSD2007-00036) from the Spanish Ministry of Science and Innovation, and the SGR programs (SGR2009-GRC703). Research in M.P.'s laboratory was supported by two grants from the Spanish Ministry of Science and Education (BIO2009-13044-C02-01 and BIO2012-31860), the framework of the XarBa, and the SGR programs (SGR2009-GRC626) from the Autonomous Government of Catalonia. Research in R.S.'s laboratory was supported by grants from the Ministry of Science and Innovation to R.S. (BIO2013-44407). M.P. and R.S. received financial support from the CONSOLIDER-INGENIO program (CSD2007-00057-B) from the Spanish Ministerio de Ciencia e Innovación. Research in the W.S. laboratory is supported by grants from the Ministry of Science and Technology and Academia Sinica. Research in phenylpropanoid gene regulation in the laboratories of E.G. and J.G. was supported by a grant from the National Science Foundation (IOS-1125620). I.-C.V.-B. was supported by a Spanish FPI Fellowship (BES-2007-17316). J.E.S.-H. was supported by the Department of Innovation, Universities and Enterprise of the Generalitatde Catalunya, the European Social Fund FI Fellowship (AGAUR: FI-2006, Resolució EDU/3600/2006; FI-2008, Resolució IUE/2658/2007 and BE-DGR2010), and CRAG.Peer reviewe

POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data

The purpose of the online resource presented here, POPcorn (Project Portal for corn), is to enhance accessibility of maize genetic and genomic resources for plant biologists. Currently, many online locations are difficult to find, some are best searched independently, and individual project websites often degrade over time—sometimes disappearing entirely. The POPcorn site makes available (1) a centralized, web-accessible resource to search and browse descriptions of ongoing maize genomics projects, (2) a single, stand-alone tool that uses web Services and minimal data warehousing to search for sequence matches in online resources of diverse offsite projects, and (3) a set of tools that enables researchers to migrate their data to the long-term model organism database for maize genetic and genomic information: MaizeGDB. Examples demonstrating POPcorn's utility are provided herein