A Combined RNA Preservation and Extraction Protocol for Gene Expression Studies in Cacao Beans

Despite the high economic importance of cacao beans, few RNA-based studies have been conducted on this plant material and hence no optimal RNA-extraction has been reported. Moreover, extraction of high-quality RNA from recalcitrant cacao bean tissue has shown many difficulties and requires optimization. Furthermore, cacao beans are mostly found at remote and under-resourced locations, which pressures the outsourcing of such analysis and thereby demands RNA-stable preservation and transportation of cacao beans. This study aims to select an appropriate RNA extraction and preservation/transportation method for cacao beans. For this purpose, three sample homogenization and five extraction protocols on cacao beans were compared. In addition, 13 preservation conditions-differing in tissue crushing degree, preservation method, duration, and temperature-were compared and evaluated. A comparative analysis revealed that CTAB-based homogenization and extraction outcompeted all tested commercial protocols in RNA yield and integrity, respectively. Preservation at -80°C affected RNA quality the least, whereas freeze-drying was most suitable for transportation at room temperature for maximum 1 week. The cacao bean RNA obtained from the selected methods were compatible for downstream applications. The results of this study will facilitate on-field sampling and transportation of genetically sensitive cacao material prior to cacao bean transcriptomic studies. In addition, valuable insights on sample homogenization, extraction, preservation, and transportation have been provided, which is of interest to every plant geneticist.

Non-volatile and volatile composition of West African bulk and Ecuadorian fine-flavor cocoa liquor and chocolate

Cocoa products are obtained from the seeds of Theobroma cacao L. In this research, cocoa liquor and chocolate produced from cocoa beans from West Africa (Forastero, "bulk" cacao) and Ecuador (Nacional variety, "fine-flavor" cacao), were investigated, using a novel approach in which various analytical techniques are combined in order to obtain in-depth knowledge of the studied cocoa samples. The levels of various classes of primary metabolites were determined and a wide range of secondary metabolites, including volatile organic acids, aldehydes, esters, pyrazines, polyphenols, methylxanthines and biogenic amines, were identified and/or quantified by HS-SPME GC-MS (headspace-solid phase microextraction gas chromatography - mass spectrometry). and UPLC-HRMS (ultra-performance liquid chromatography - high resolution mass spectrometry). Odor Activity Values (OAV) were calculated to assess the contribution of individual volatiles on the final aroma. Various volatile aroma compounds were more abundant in the West African cocoa liquor and chocolate, while the Ecuadorian samples were richer in most quantified non-volatile metabolites. Principal component analysis (PCA) confirmed that the four samples can be clearly distinguished. Alcohols, pyrazines, amino acids and biogenic amines were found to be highly influential in causing this differentiation. The proposed approach can be useful in future studies on more extensive cocoa sample collections, in order to highlight similarities and pinpoint typical differences in chemical composition among these samples.

The development of a novel SNP genotyping assay to differentiate cacao clones

In this study, a double-mismatch allele-specific (DMAS) qPCR SNP genotyping method has been designed, tested and validated specifically for cacao, using 65 well annotated international cacao reference accessions retrieved from the Center for Forestry Research and Technology Transfer (CEFORTT) and the International Cocoa Quarantine Centre (ICQC). In total, 42 DMAS-qPCR SNP genotyping assays have been validated, with a 98.05% overall efficiency in calling the correct genotype. In addition, the test allowed for the identification of 15.38% off-types and two duplicates, highlighting the problem of mislabeling in cacao collections and the need for conclusive genotyping assays. The developed method showed on average a high genetic diversity (H_e = 0.416) and information index (I = 0.601), making it applicable to assess intra-population variation. Furthermore, only the 13 most informative markers were needed to achieve maximum differentiation. This simple, effective method provides robust and accurate genotypic data which allows for more efficient resource management (e.g. tackling mislabeling, conserving valuable genetic material, parentage analysis, genetic diversity studies), thus contributing to an increased knowledge on the genetic background of cacao worldwide. Notably, the described method can easily be integrated in other laboratories for a wide range of objectives and organisms.

Assessing the influence of pod storage on sugar and free amino acid profiles and the implications on some Maillard reaction related flavor volatiles in Forastero cocoa beans

The practice of pod storage (PS) has been applied in many cocoa producing countries, especially by Ghanaian farmers over the years. However, the study of PS has not received much attention, hence, until now, its potential impact on specific flavor precursor development and implications on the flavor of cocoa beans still remains uncovered. The study was therefore aimed at exploring this possibility through physico-chemical and flavor precursor analyses, carried out on equally fermented and dried pod stored (0, 3 and 7 days) Ghanaian cocoa beans. Flavor analysis was also conducted on equally roasted pod stored cocoa beans. Through visual assessment of the pods, pulp and beans, the compelling impact of PS on fermentation index (FI) and nib acidity could be demonstrated by the various biochemical and physical changes such as respiration, moisture reduction, and cellular degradation, occurring during the process. Whereas the entire reaction of sugar degradation may be deemed complex, a clear relationship between the FI, nib acidity and the glucose content was observed. Also, PS was found to increase with marginal increase in total reducing sugars (glucose and fructose). Although the concentration of free amino acids was directly proportional to the duration of PS, within the framework of this study, a significant difference (p < .05) was only observed in the case of extended duration (7 days). Overall, 7 PS seemed to have enhanced the formation of more volatiles. This was followed by 0 PS and finally 3 PS. Suggestively, these findings could provide some indications in explaining the typical flavor profiles of the Ghanaian cocoa beans, considering the fact that 87.8% of Ghanaian farmers adhere to this practice. Meanwhile, for the chocolate industry, the surging demand for cocoa/chocolate products exhibiting unique flavors, could be partly addressed by adopting PS as a tool for varietizing the flavor capacity of "bulk" cocoa through the expression or suppression of specific flavor precursors in the raw material on the farm level, which comes with almost no additional cost.

Quantitative and Functional Requirements for Bioluminescent Cancer Models

BACKGROUND

Bioluminescent cancer models are widely used but detailed quantification of the luciferase signal and functional comparison with a non-transfected control cell line are generally lacking. In the present study, we provide quantitative and functional tests for luciferase-transfected cells.

MATERIALS AND METHODS

We quantified the luciferase expression in BLM and HCT8/E11 transfected cancer cells, and examined the effect of long-term luciferin exposure. The present study also investigated functional differences between parental and transfected cancer cells.

RESULTS

Our results showed that quantification of different single-cell-derived populations are superior with droplet digital polymerase chain reaction. Quantification of luciferase protein level and luciferase bioluminescent activity is only useful when there is a significant difference in copy number. Continuous exposure of cell cultures to luciferin leads to inhibitory effects on mitochondrial activity, cell growth and bioluminescence. These inhibitory effects correlate with luciferase copy number. Cell culture and mouse xenograft assays showed no significant functional differences between luciferase-transfected and parental cells.

CONCLUSION

Luciferase-transfected cells should be validated by quantitative and functional assays before starting large-scale experiments.

DTREEv2, a computer-based support system for the risk assessment of genetically modified plants

Risk assessment of genetically modified organisms (GMOs) remains a contentious area and a major factor influencing the adoption of agricultural biotech. Methodologically, in many countries, risk assessment is conducted by expert committees with little or no recourse to databases and expert systems that can facilitate the risk assessment process. In this paper we describe DTREEv2, a computer-based decision support system for the identification of hazards related to the introduction of GM-crops into the environment. DTREEv2 structures hazard identification and evaluation by means of an Event-Tree type of analysis. The system produces an output flagging identified hazards and potential risks. It is intended to be used for the preparation and evaluation of biosafety dossiers and, as such, its usefulness extends to researchers, risk assessors and regulators in government and industry.

Detection of soy DNA in margarines

The method in which to discriminate between genetically modified (GM) versus non-modified foodstuffs is based on the presence of newly introduced genes at the protein or DNA level. Current available methods are almost exclusively based on the polymerase chain reaction (PCR). This procedure consists of three steps: DNA isolation, the amplification of the desired DNA fragment and visualisation of the obtained amplification products. The first and crucial step is the DNA isolation. Due to several processing steps, the quality of the extracted DNA may be damaged, rendering PCR analysis, and therefore GMO detection, impossible. In this study, the DNA quality of soy lecithin in margarines has been evaluated by PCR. For this purpose, DNA was isolated from margarines with different levels of lecithin with two different extraction methods, including the CTAB method proposed by the European Committe for Standardization (CEN). The amplification of soy DNA by PCR resulted to be difficult, which could be explained by the difficult DNA extraction from margarine and the low lecithin content.

Extraction and PCR analysis of soy DNA in chocolate

The manner in which to discriminate between genetically modified (GM) versus non-modified foodstuffs is based on the presence of newly introduced genes at the protein or DNA level. Current available methods are almost exclusively based on the polymerase chain reaction (PCR). These methods consist of three steps: DNA isolation, amplification of the desired DNA fragment and visualisation of the obtained amplification products. The first and crucial step is the DNA isolation. In this study three different methods are described for the isolation of DNA from chocolate, two of which are commercial kits. The results indicate that both kits, in contrast with the non-commercial method, are suitable for the isolation of DNA from chocolate, provided that the adapted PCR conditions are applied.

Heterogeneous photobleaching in confocal microscopy caused by differences in refractive index and excitation mode

The photobleaching of fluorescence emission during confocal laser scanning was studied on well-defined, stained objects [microspheres of polystyrene or fluorescent gels of fluorescein isothiocyanate (FITC)-labeled dextran] and on biological samples. X,Y laser scanning with confocal microscopy induces fundamental differences in exposure rate and time in different z-planes orthogonal to the optical axis. A heterogeneous bleaching rate was observed at different focal levels in the polystyrene spheres and in the gels. This phenomenon can be caused by refractive index differences or is correlated with a photobleaching rate, which is dependent not only on the excitation light intensity but also on the photon flux (total intensity per unit of time). Heterogeneous excitation induced by refractive index differences results in photobleaching differences but will not necessarily cause heterogeneous emission intensity. Altered emission originating from altered excitation will be annihilated if the emitted light returns to the image plane along the same inverse path, compensating for the proportional increase or decrease in excitation intensity with an increased or decreased emission intensity. High numerical aperture or increased scanning speed increases the photobleaching rate. This leads to the conclusion that photobleaching in confocal scanning laser microscopy is dependent on photon energy flux density (joule/m2s).