A panel of the most suitable reference genes for RT-qPCR expression studies of coffee: screening their stability under different conditions

The reliability of analyses using real-time quantitative polymerase chain reaction (RT-qPCR) depends on the selection of appropriate reference genes to correct for sample-to-sample and run-to-run variations. The aim of the present study was to select the most suitable reference genes for gene expression analyses in tissue samples from coffee, Coffea arabica L. (Arabica) grown under well-watered (WW) and water-deficit (WD) conditions and C. canephora Pierre ex A. Froehner (Robusta) grown under WW conditions. Expression profiles and stabilities were evaluated for 12 reference genes in different tissues from C. arabica and for 8 genes in tissues from C. canephora. The web-based RefFinder tool, which combines the geNorm, NormFinder, Bestkeeper, and Delta-Ct algorithms, was employed to assess the stability of the tested genes. The most stable reference genes identified for all tissues grouped (WW/WD) of C. arabica were clathrin adaptor protein medium subunit (AP47), ubiquitin (UBQ), 60S ribosomal protein L39 (RPL39), and elongation factor 1α (EF1α), while class III alcohol dehydrogenase (ADH2), β-actin (ACT), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and ubiquitin (UBQ) genes were the most stable for all tissues grouped (WW) of C. canephora tissues. Validation by the expression level analysis of CaACO-like demonstrated that the use of the best and the worst set of reference genes produced different expression results. The results reinforce the general assumption that there is no universal reference gene and that it is essential to select the most appropriate gene for each individual experiment to apply adequate normalization procedures of RT-qPCR data.     

Ecto-5′-nucleotidase/CD73 knockdown increases cell migration and mRNA level of collagen I in a hepatic stellate cell line

Ecto-5′-nucleotidase (eNT/CD73, E.C.3.1.3.5) is a glycosyl phosphatidylinositol (GPI)-linked cell-surface protein with several functions, including the local generation of adenosine from AMP, with the consequent activation of adenosine receptors and the salvaging of extracellular nucleotides. It also apparently functions independently of this activity, e.g., in the mediation of cell-cell adhesion. Liver fibrosis can be considered as a dynamic and integrated cellular response to chronic liver injury and the activation of hepatic stellate cells (HSCs) plays a role in the fibrogenic process. eNT/CD73 and adenosine are reported to play an important role in hepatic fibrosis in murine models. Knockdown of eNT/CD73 leads to an increase in mRNA expression of tissue non-specific alkaline phosphatase (TNALP), another AMP-degrading enzyme and thus no alteration is seen in the total ecto-AMPase activity of the cell. eNT/CD73 knockdown also leads to changes in the expression of collagen I and a clear alteration of cell migration. We suggest that eNT/CD73 protein expression controls cell migration and collagen expression in a mechanism independent of changes in nucleotide metabolism.     

Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan

Background

Aluminum (Al) toxicity is an important limitation to food security in tropical and subtropical regions. High Al saturation on acid soils limits root development, reducing water and nutrient uptake. In addition to naturally occurring acid soils, agricultural practices may decrease soil pH, leading to yield losses due to Al toxicity. Elucidating the genetic and molecular mechanisms underlying maize Al tolerance is expected to accelerate the development of Al-tolerant cultivars.

Results

Five genomic regions were significantly associated with Al tolerance, using 54,455 SNP markers in a recombinant inbred line population derived from Cateto Al237. Candidate genes co-localized with Al tolerance QTLs were further investigated. Near-isogenic lines (NILs) developed for ZmMATE2 were as Al-sensitive as the recurrent line, indicating that this candidate gene was not responsible for the Al tolerance QTL on chromosome 5, qALT5. However, ZmNrat1, a maize homolog to OsNrat1, which encodes an Al³⁺ specific transporter previously implicated in rice Al tolerance, was mapped at ~40 Mbp from qALT5. We demonstrate for the first time that ZmNrat1 is preferentially expressed in maize root tips and is up-regulated by Al, similarly to OsNrat1 in rice, suggesting a role of this gene in maize Al tolerance. The strongest-effect QTL was mapped on chromosome 6 (qALT6), within a 0.5 Mbp region where three copies of the Al tolerance gene, ZmMATE1, were found in tandem configuration. qALT6 was shown to increase Al tolerance in maize; the qALT6-NILs carrying three copies of ZmMATE1 exhibited a two-fold increase in Al tolerance, and higher expression of ZmMATE1 compared to the Al sensitive recurrent parent. Interestingly, a new source of Al tolerance via ZmMATE1 was identified in a Brazilian elite line that showed high expression of ZmMATE1 but carries a single copy of ZmMATE1.

Conclusions

High ZmMATE1 expression, controlled either by three copies of the target gene or by an unknown molecular mechanism, is responsible for Al tolerance mediated by qALT6. As Al tolerant alleles at qALT6 are rare in maize, marker-assisted introgression of this QTL is an important strategy to improve maize adaptation to acid soils worldwide.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-153) contains supplementary material, which is available to authorized users.     

The use of electromyography for the assessment of sense of muscular effort: a test–retest reliability study

This study sought to examine the test–retest reliability to measure sense of muscular effort with electromyography (EMG). The EMG activity of the tibialis anterior muscle from 23 participants was recorded. Targets of EMG amplitudes produced at 10 and 20% of the maximum voluntary contraction (MVC) were calculated. Participants matched the target EMG level with and without visual feedback (FB). With NFB, the reliability was good to excellent when errors were represented as the average standard deviation (SD) of the error from the target (ICC_1,2 = 0.75 and 0.69 for 10 and 20% targets, respectively). Also, reliability was good when errors were presented as the average SD as a percentage of the MVC EMG (intraclass correlation coefficient (ICC_1,2) = 0.67 and 0.66, respectively, for 10 and 20% targets). Standard deviation around the target was the most reliable method to represent the error. This approach could be used as a simple cost-effective method to assess the sense of muscular effort.     

Co-packaging of sense and antisense RNAs: a novel strategy for blocking HIV-1 replication.

Retroviral vectors were engineered to express either sense (MoTiN-TRPsie+) or sense and antisense (MoTN-TRPsie+/-) RNAs containing the human immunodeficiency virus type-1 (HIV-1) trans -activation response (TAR) element and the extended packaging (Psie) signal. The Psie signal includes the dimer linkage structure (DLS) and the Rev response element (RRE). Amphotropic vector particles were used to transduce a human CD4+ T-lymphoid (MT4) cell line. Stable transductants were then tested for sense and antisense RNA production and susceptibility to HIV-1 infection. HIV-1 production was significantly decreased in cells transduced with MoTiN-TRPsie+ and MoTN-TRPsie+/-vectors. Efficient packaging of sense and most remarkably of antisense RNA was observed within the virus progeny. Infectivity of this virus was significantly decreased in both cases, suggesting that the interfering RNAs were co-packaged with HIV-1 RNA. Vector transduction was not expected to occur and was not observed. Inhibition of HIV-1 replication was also demonstrated in human peripheral blood lymphocytes transduced with retroviral vectors expressing antisense RNA. These results suggest that (i) both sense and antisense RNAs were co-packaged with HIV-1 RNA, (ii) the co-packaged sense and antisense RNAs inhibited virus infectivity and (iii) the co-packaged sense and antisense RNAs were not transduced. Sense and antisense RNA-based strategies may also be used to co-package other interfering RNAs (e.g. ribozymes) to cleave HIV-1 virion RNA.     

The myelin-associated glycoprotein is phosphorylated in the peripheral nervous system.

Phosphorylation of the myelin-associated glycoprotein (MAG) in the peripheral nervous system is demonstrated by immunoprecipitation from myelin proteins radiolabeled in vivo, in nerve slices and in a cell-free system. Phosphoamino acid analysis of immunoprecipitated MAG revealed the presence of radioactivity in phosphoserine, but not in phosphothreonine or phosphotyrosine. Only the shorter isoform of MAG (S-MAG) was detected by immunostaining of nitrocellulose sheets with anti-MAG anti-serum after enzymatic deglycosylation of immunoprecipitated MAG labeled in nerve slices. Autoradiography of the same Western blots revealed that most of the radioactive phosphate was in S-MAG, demonstrating that the polypeptide backbone of S-MAG is phosphorylated in the PNS.     

Autoradiographic analysis of Schistosoma mansoni migration in the NZ rabbit

The migration of larval Schistosoma mansoni was tracked by means of autoradiographic analysis in naive rabbits percutaneously exposed to L-(75Se) selenomethionine-labeled cercariae on serial intervals of 1, 2, 4, 6, 8, 10, 15, 20, 25, 30, 40 and 50 days post-infection. Autoradiographic foci were detected from the 1st day in the skin, up to the 15th day in the liver. Adult and mature worms were recovered either paired or not 60 days after infection, by perfusion of hepatic and mesenteric veins. Morphometric analysis under optical microscopy, showed that worms were within regular dimention limits as compared to adult worms harboured by other host species. These observations extend previous informations on the S. mansoni-rabbit association and clearly demonstrate the post-liver phase of S. mansoni life-cycle in this host.