Attenuated total reflection Fourier-transform infrared spectroscopy reveals environment specific phenotypes in clonal Japanese knotweed.

BACKGROUND: Japanese knotweed (Reynoutria japonica var. japonica), a problematic invasive species, has a wide geographical distribution. We have previously shown the potential for attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy and chemometrics to segregate regional differentiation between Japanese knotweed plants. However, the contribution of environment to spectral differences remains unclear. Herein, the response of Japanese knotweed to varied environmental habitats has been studied. Eight unique growth environments were created by manipulation of the red: far-red light ratio (R: FR), water availability, nitrogen, and micronutrients. Their impacts on plant growth, photosynthetic parameters, and ATR-FTIR spectral profiles, were explored using chemometric techniques, including principal component analysis (PCA), linear discriminant analysis, support vector machines (SVM) and partial least squares regression. Key wavenumbers responsible for spectral differences were identified with PCA loadings, and molecular biomarkers were assigned. Partial least squared regression (PLSR) of spectral absorbance and root water potential (RWP) data was used to create a predictive model for RWP. RESULTS: Spectra from plants grown in different environments were differentiated using ATR-FTIR spectroscopy coupled with SVM. Biomarkers highlighted through PCA loadings corresponded to several molecules, most commonly cell wall carbohydrates, suggesting that these wavenumbers could be consistent indicators of plant stress across species. R: FR most affected the ATR-FTIR spectra of intact dried leaf material. PLSR prediction of root water potential achieved an R2 of 0.8, supporting the potential use of ATR-FTIR spectrometers as sensors for prediction of plant physiological parameters. CONCLUSIONS: Japanese knotweed exhibits environmentally induced phenotypes, indicated by measurable differences in their ATR-FTIR spectra. This high environmental plasticity reflected by key biomolecular changes may contribute to its success as an invasive species. Light quality (R: FR) appears critical in defining the growth and spectral response to environment. Cross-species conservation of biomarkers suggest that they could function as indicators of plant-environment interactions including abiotic stress responses and plant health.

Attenuated total reflection Fourier-transform infrared spectroscopy for the prediction of hormone concentrations in plants.

Plant hormones are important in the control of physiological and developmental processes including seed germination, senescence, flowering, stomatal aperture, and ultimately the overall growth and yield of plants. Many currently available methods to quantify such growth regulators quickly and accurately require extensive sample purification using complex analytic techniques. Herein we used ultra-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) to create and validate the prediction of hormone concentrations made using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectral profiles of both freeze-dried ground leaf tissue and extracted xylem sap of Japanese knotweed (Reynoutria japonica) plants grown under different environmental conditions. In addition to these predictions made with partial least squares regression, further analysis of spectral data was performed using chemometric techniques, including principal component analysis, linear discriminant analysis, and support vector machines (SVM). Plants grown in different environments had sufficiently different biochemical profiles, including plant hormonal compounds, to allow successful differentiation by ATR-FTIR spectroscopy coupled with SVM. ATR-FTIR spectral biomarkers highlighted a range of biomolecules responsible for the differing spectral signatures between growth environments, such as triacylglycerol, proteins and amino acids, tannins, pectin, polysaccharides such as starch and cellulose, DNA and RNA. Using partial least squares regression, we show the potential for accurate prediction of plant hormone concentrations from ATR-FTIR spectral profiles, calibrated with hormonal data quantified by UHPLC-HRMS. The application of ATR-FTIR spectroscopy and chemometrics offers accurate prediction of hormone concentrations in plant samples, with advantages over existing approaches.

Regional differences in clonal Japanese knotweed revealed by chemometrics-linked attenuated total reflection Fourier-transform infrared spectroscopy.

BACKGROUND: Japanese knotweed (R. japonica var japonica) is one of the world's 100 worst invasive species, causing crop losses, damage to infrastructure, and erosion of ecosystem services. In the UK, this species is an all-female clone, which spreads by vegetative reproduction. Despite this genetic continuity, Japanese knotweed can colonise a wide variety of environmental habitats. However, little is known about the phenotypic plasticity responsible for the ability of Japanese knotweed to invade and thrive in such diverse habitats. We have used attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy, in which the spectral fingerprint generated allows subtle differences in composition to be clearly visualized, to examine regional differences in clonal Japanese knotweed. RESULTS: We have shown distinct differences in the spectral fingerprint region (1800-900 cm- 1) of Japanese knotweed from three different regions in the UK that were sufficient to successfully identify plants from different geographical regions with high accuracy using support vector machine (SVM) chemometrics. CONCLUSIONS: These differences were not correlated with environmental variations between regions, raising the possibility that epigenetic modifications may contribute to the phenotypic plasticity responsible for the ability of R. japonica to invade and thrive in such diverse habitats.

Treating seeds with activators of plant defence generates long-lasting priming of resistance to pests and pathogens.

• Priming of defence is a strategy employed by plants exposed to stress to enhance resistance against future stress episodes with minimal associated costs on growth. Here, we test the hypothesis that application of priming agents to seeds can result in plants with primed defences. • We measured resistance to arthropod herbivores and disease in tomato (Solanum lycopersicum) plants grown from seed treated with jasmonic acid (JA) and/or ß-aminobutryric acid (BABA). • Plants grown from JA-treated seed showed increased resistance against herbivory by spider mites, caterpillars and aphids, and against the necrotrophic fungal pathogen, Botrytis cinerea. BABA seed treatment provided primed defence against powdery mildew disease caused by the biotrophic fungal pathogen, Oidium neolycopersici. Priming responses were long-lasting, with significant increases in resistance sustained in plants grown from treated seed for at least 8 wk, and were associated with enhanced defence gene expression during pathogen attack. There was no significant antagonism between different forms of defence in plants grown from seeds treated with a combination of JA and BABA. • Long-term defence priming by seed treatments was not accompanied by reductions in growth, and may therefore be suitable for commercial exploitation.

Histone H4K20me3 and HP1α are late heterochromatin markers in development, but present in undifferentiated embryonic stem cells.

We report here that the formation of heterochromatin in cell nuclei during mouse development is characterised by dynamic changes in the epigenetic modifications of histones. Our observations reveal that heterochromatin in mouse preimplantation embryos is in an immature state that lacks the constitutive heterochromatin markers histone H4 trimethyl Lys20 (H4K20me3) and chromobox homolog 5 (HP1α, also known as CBX5). Remarkably, these somatic heterochromatin hallmarks are not detectable--except in mural trophoblast--until mid-gestation, increasing in level during foetal development. Our results support a developmentally regulated connection between HP1α and H4K20me3. Whereas inner cell mass (ICM) and epiblast stain negative for H4K20me3 and HP1α, embryonic stem (ES) cell lines, by contrast, stain positive for these markers, indicating substantial chromatin divergence. We conclude that H4K20me3 and HP1α are late developmental epigenetic markers, and slow maturation of heterochromatin in tissues that develop from ICM is ectopically induced during ES cell derivation. Our findings suggest that H4K20me3 and HP1α are markers for cell type commitment that can be triggered by developmental or cell context, independently of the differentiation process.

Biogenic volatile organic compounds in the Earth system.

Biogenic volatile organic compounds produced by plants are involved in plant growth, development, reproduction and defence. They also function as communication media within plant communities, between plants and between plants and insects. Because of the high chemical reactivity of many of these compounds, coupled with their large mass emission rates from vegetation into the atmosphere, they have significant effects on the chemical composition and physical characteristics of the atmosphere. Hence, biogenic volatile organic compounds mediate the relationship between the biosphere and the atmosphere. Alteration of this relationship by anthropogenically driven changes to the environment, including global climate change, may perturb these interactions and may lead to adverse and hard-to-predict consequences for the Earth system.

Discrimination of plant volatile signatures by an electronic nose: aA potential technology for plant pest and disease monitoring.

The volatile organic compounds (VOCs) profile emitted from plants often changes in response to environmental factors, and monitoring the change of such profiles could provide a nondestructive means of plant health measurement An electronic nose (e-nose) was used to discriminate among VOC bouquets emitted by cucumber, pepper, and tomato leaves subjected to mechanical damage or pest and disease attacks compared with undamaged control leaves. Principle component analysis, discriminant function analysis, and cluster analysis were applied to evaluate the data. The results indicate that the e-nose can discriminate among VOCs from undamaged leaves of the three tested species. It can also discriminate undamaged and artificially damaged leaves of the same plant species. In cucumber, the e-nose can discriminate among VOCs emitted from control, artificially damaged, and spider-mite-infested leaves. It could also discriminate among VOCs emitted from control, artificially damaged, hornworm-damaged, and powdery-mildew-infected tomato leaves. The relationships between the changes in volatile signatures detected by the e-nose to changes in the underlying chemistry of plant VOC signatures in response to applied stresses were quantified by gas chromatography mass spectrometry. We conclude that the e-nose had genuine responses to changes in plant VOC signatures and can successfully discriminate them. These studies demonstrate the potential use of such e-nose technology as a real time pest and disease monitoring system in agricultural and horticultural settings.

Isoprene emissions influence herbivore feeding decisions.

Isoprene (C(5)H(8), 2-methyl 1,3-butadiene) is synthesized and emitted by many, but not all, plants. Unlike other related volatile organic compounds (monoterpenes and sesquiterpenes), isoprene has not been shown to mediate plant-herbivore interactions. Here, for the first time, we show, in feeding choice tests using isoprene-emitting transgenic tobacco plants (Nicotiana tabacum cv. Samsun) and non-emitting azygous control plants, that isoprene deters Manduca sexta caterpillars from feeding. This avoidance behaviour was confirmed using an artificial (isoprene-emitting and non-emitting control) diet. Both in vivo and in vitro experiments showed that isoprene can activate feeding avoidance behaviour in this system with a dose-response effect on caterpillar behaviour and an isoprene emission threshold level of <6 nmol m(-2) s(-1).

The role of isoprene in insect herbivory.

Several hypotheses have previously been proposed to explain the function of isoprene in plants, including its ability to protect the leaf metabolic machinery from transient high temperature1,2 and from oxidative stress.3 Isoprene may also serve as a metabolic overflow mechanism for carbon or photosynthetic energy4-6 and may promote flowering in neighbouring plants.7 We have reported recently that isoprene can be detected by a herbivore, Manduca sexta, and that it directly deters them from feeding, with an isoprene emission threshold level of <6 nmol m(-2) s(-1).8 We demonstrated this using both in vivo experiments, using isoprene-emitting transgenic tobacco plants (Nicotiana tabacum cv. Samsun) and non-emitting azygous control plants, and in vitro experiments, using an artificial (isoprene-emitting and non-emitting control) diet. Here we discuss the potential role of isoprene in plant-herbivore interactions and the possibility that isoprene actually serves multiple purposes in plants.

Effect of zona pellucida removal on DNA methylation in early mouse embryos.

Removal of the zona pellucida is known to affect mouse development to term. Zygotes were recovered immediately after fertilization and their zona pellucida removed by exposure to pronase before culture and comparison with zona-intact embryos. The effect of removing the zona pellucida was assessed in terms of embryo development to blastocyst, DNA methylation, histone acetylation, and expression of three developmentally regulated genes. No significant differences were seen in percentage of embryos that developed to the blastocyst stage. However, zona-free embryos showed a significant reduction in the DNA methylation level at two-cell and four-cell stages, but no differences at pronuclear, morula, and blastocyst stages, as observed by immunofluorescence. Mechanical or enzymatic removal of the zona pellucida showed similar DNA methylation staining patterns at the two-cell stage. The time when the zona pellucida was removed appears to influence the levels of DNA methylation. When zona removal was delayed for 8 h, there was no difference in DNA methylation levels between zona-free and zona-intact two-cell embryos, indicating that the critical time is early on, between 1 and 8 h postfertilization. In contrast, when immunofluorescence analysis of histone acetylation was performed, no significant differences were seen between zona-free and zona-intact embryos at any of the developmental stage. Similarly, no differences were found regarding the onset of transcription of Dnmt1s, Nanog, and Fgf4 genes.

Live lambs born from zona-pellucida denuded embryos.

Progress with techniques using zona-pellucida denuded embryos has resulted in the birth of live cattle, pigs, and mice. The application of zona-free methods in sheep has been restricted to in vitro studies. In this report, we demonstrate that live lambs can be produced from zona-free IVF embryos. We are pursuing this method as a prerequisite to developing viral vector co-culture delivery strategies.

The effect of interspecific oocytes on demethylation of sperm DNA.

In contrast to mice, in sheep no genome-wide demethylation of the paternal genome occurs within the first postfertilization cell cycle. This difference could be due either to an absence of a sheep demethylase activity that is present in mouse ooplasm or to an increased protection of methylated cytosine residues in sheep sperm. Here, we use interspecies intracytoplasmic sperm injection to demonstrate that sheep sperm DNA can be demethylated in mouse oocytes. Surprisingly, mouse sperm can also be demethylated to a limited extent in sheep oocytes. Our results suggest that the murine demethylation process is facilitated either by a sperm-derived factor or by male pronuclear chromatin composition.

Signalling crosstalk in plants: emerging issues.

The Oxford English Dictionary defines crosstalk as 'unwanted transfer of signals between communication channels'. How does this definition relate to the way in which we view the organization and function of signalling pathways? Recent advances in the field of plant signalling have challenged the traditional view of a signalling transduction cascade as isolated linear pathways. Instead the picture emerging of the mechanisms by which plants transduce environmental signals is of the interaction between transduction chains. The manner in which these interactions occur (and indeed whether the transfer of these signals is 'unwanted' or beneficial) is currently the topic of intense research.

Crosstalk between plant responses to pathogens and herbivores: a view from the outside in.

Plants encounter numerous pests and pathogens in the natural environment. An appropriate response to attack by such organisms can lead to tolerance or resistance mechanisms that enable the plant to survive. Many studies concentrate on the signalling pathways that enable plants to recognize and respond to attack, and measure the downstream effect in either biochemical or molecular terms. At the whole plant level, ecologists examine the fitness costs of attack not only for the plant but also over a range of trophic levels. The links between these differing levels of study are beginning to be addressed by the adoption of molecular approaches in more ecologically relevant settings. This review will describe the different approaches used by ecologists and cell biologists in this field and will try to address the question of how we can explore the response to, and consequences, of attack by multiple enemies.

Human cloning: can it be made safe?

There are continued claims of attempts to clone humans using nuclear transfer, despite the serious problems that have been encountered in cloning other mammals. It is known that epigenetic and genetic mechanisms are involved in clone failure, but we still do not know exactly how. Human reproductive cloning is unethical, but the production of cells from cloned embryos could offer many potential benefits. So, can human cloning be made safe?

Thermotolerant guard cell protoplasts of tree tobacco do not require exogenous hormones to survive in culture and are blocked from reentering the cell cycle at the G1-to-S transition.

When guard cell protoplasts (GCPs) of tree tobacco [Nicotiana glauca (Graham)] are cultured at 32 degrees C with an auxin (1-napthaleneacetic acid) and a cytokinin (6-benzylaminopurine), they reenter the cell cycle, dedifferentiate, and divide. GCPs cultured similarly but at 38 degrees C and with 0.1 micro M +/- -cis,trans-abscisic acid (ABA) remain differentiated. GCPs cultured at 38 degrees C without ABA dedifferentiate partially but do not divide. Cell survival after 1 week is 70% to 80% under all of these conditions. In this study, we show that GCPs cultured for 12 to 24 h at 38 degrees C accumulate heat shock protein 70 and develop a thermotolerance that, upon transfer of cells to 32 degrees C, enhances cell survival but inhibits cell cycle reentry, dedifferentiation, and division. GCPs dedifferentiating at 32 degrees C require both 1-napthaleneacetic acid and 6-benzylaminopurine to survive, but thermotolerant GCPs cultured at 38 degrees C +/- ABA do not require either hormone for survival. Pulse-labeling experiments using 5-bromo-2-deoxyuridine indicate that culture at 38 degrees C +/- ABA prevents dedifferentiation of GCPs by blocking cell cycle reentry at G1/S. Cell cycle reentry at 32 degrees C is accompanied by loss of a 41-kD polypeptide that cross-reacts with antibodies to rat (Rattus norvegicus) extracellular signal-regulated kinase 1; thermotolerant GCPs retain this polypeptide. A number of polypeptides unique to thermotolerant cells have been uncovered by Boolean analysis of two-dimensional gels and are targets for further analysis. GCPs of tree tobacco can be isolated in sufficient numbers and with the purity required to study plant cell thermotolerance and its relationship to plant cell survival, growth, dedifferentiation, and division in vitro.