Analysing growth and development of plants jointly using developmental growth stages

Background and Aims Plant growth, the increase of organ dimensions over time, and development, the change in plant structure, are often studied as two separate processes. However, there is structural and functional evidence that these two processes are strongly related. The aim of this study was to investigate the co-ordination between growth and development using mango trees, which have well-defined developmental stages.Methods Developmental stages, determined in an expert way, and organ sizes, determined from objective measurements, were collected during the vegetative growth and flowering phases of two cultivars of mango, Mangifera indica. For a given cultivar and growth unit type (either vegetative or flowering), a multistage model based on absolute growth rate sequences deduced from the measurements was first built, and then growth stages deduced from the model were compared with developmental stages.Key Results Strong matches were obtained between growth stages and developmental stages, leading to a consistent definition of integrative developmental growth stages. The growth stages highlighted growth asynchronisms between two topologically connected organs, namely the vegetative axis and its leaves.Conclusions Integrative developmental growth stages emphasize that developmental stages are closely related to organ growth rates. The results are discussed in terms of the possible physiological processes underlying these stages, including plant hydraulics, biomechanics and carbohydrate partitioning.     

Widespread parallel population adaptation to climate variation across a radiation: implications for adaptation to climate change

Global warming will impact species in a number of ways, and it is important to know the extent to which natural populations can adapt to anthropogenic climate change by natural selection. Parallel microevolution within separate species can demonstrate natural selection, but several studies of homoplasy have not yet revealed examples of widespread parallel evolution in a generic radiation. Taking into account primary phylogeographic divisions, we investigate numerous quantitative traits (size, shape, scalation, colour pattern and hue) in anole radiations from the mountainous Lesser Antillean islands. Adaptation to climatic differences can lead to very pronounced differences between spatially close populations with all studied traits showing some evidence of parallel evolution. Traits from shape, scalation, pattern and hue (particularly the latter) show widespread evolutionary parallels within these species in response to altitudinal climate variation greater than extreme anthropogenic climate change predicted for 2080. This gives strong evidence of the ability to adapt to climate variation by natural selection throughout this radiation. As anoles can evolve very rapidly, it suggests anthropogenic climate change is likely to be less of a conservation threat than other factors, such as habitat loss and invasive species, in this, Lesser Antillean, biodiversity hot spot.     

Energy expenditure during tennis play: a preliminary video analysis and metabolic model approach

The aim of this study was to estimate, using video analysis, what proportion of the total energy expenditure during a tennis match is accounted for by aerobic and anaerobic metabolism, respectively. The method proposed involved estimating the metabolic power (MP) of 5 activities, which are inherent to tennis: walking, running, hitting the ball, serving, and sitting down to rest. The energy expenditure concerned was calculated by sequencing the activity by video analysis. A bioenergetic model calculated the aerobic energy expenditure (EEO2mod) in terms of MP, and the anaerobic energy expenditure was calculated by subtracting this (MP - EEO2mod). Eight tennis players took part in the experiment as subjects (mean ± SD: age 25.2 ± 1.9 years, weight 79.3 ± 10.8 kg, VO2max 54.4 ± 5.1 ml·kg(-1)·min(-1)). The players started off by participating in 2 games while wearing the K4b2, with their activity profile measured by the video analysis system, and then by playing a set without equipment but with video analysis. There was no significant difference between calculated and measured oxygen consumptions over the 16 games (p = 0.763), and these data were strongly related (r = 0.93, p < 0.0001). The EEO2mod was quite weak over all the games (49.4 ± 4.8% VO2max), whereas the MP during points was up to 2 or 3 times the VO2max. Anaerobic metabolism reached 32% of the total energy expenditure across all the games 67% for points and 95% for hitting the ball. This method provided a good estimation of aerobic energy expenditure and made it possible to calculate the anaerobic energy expenditure. This could make it possible to estimate the metabolic intensity of training sessions and matches using video analysis.     

A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation

Reverse complementary DNA sequences––sequences that are inadvertently cast backward and in which all purines and pyrimidines are transposed––are not uncommon in sequence databases, where they may introduce noise into sequence-based research. We show that about 1% of the public fungal ITS sequences, the most commonly sequenced genetic marker in mycology, are reverse complementary, and we introduce an open source software solution to automate their detection and reorientation. The MacOSX/Linux/UNIX software operates on public or private datasets of any size, although some 50 base pairs of the 5.8S gene of the ITS region are needed for the analysis.     

Succinimidyl residue formation in hen egg-white lysozyme favors the formation of intermolecular covalent bonds without affecting its tertiary structure

Protein chemical degradations occur naturally into living cells as soon as proteins have been synthesized. Among these modifications, deamidation of asparagine or glutamine residues has been extensively studied, whereas the intermediate state, a succinimide derivative, was poorly investigated because of the difficulty of isolating those transient species. We used an indirect method, a limited thermal treatment in the dry state at acidic pH, to produce stable cyclic imide residues in hen lysozyme molecules, enabling us to examine the structural and functional properties of so modified proteins. Five cyclic imide rings have been located at sites directly accessible to solvent and did not lead to any changes in secondary or tertiary structures. However, they altered the catalytic properties of lysozyme and significantly decreased the intrinsic stability of the molecules. Moreover, dimerization occurred during the treatment, and this phenomenon was proportional to the extent of chemical degradation. We propose that succinimide formation could be responsible for covalent bond formation under specific physicochemical conditions that could be found in vivo.     

Incidental findings in data-intensive postgenomics science and legal liability of clinician-researchers: ready for vaccinomics?

Vaccinomics encompasses a host of multiomics approaches to characterize variability in host-environment (including pathogens) interactions, with a view to a more directed or personalized use of vaccine-based health interventions. Although vaccinomics has the potential to reduce adverse effects and increase efficacy of vaccines, the use of high-throughput, data-intensive technologies may also lead to unanticipated discoveries beyond the initial aims of a vaccinomics study--discoveries that could be highly significant to the health of the research participants. How do clinician-researchers faced with such information have to act? What are the attendant legal duties in such circumstances and how do they differ from the duties of non-clinician researchers? Together with a critical analysis of the international laws and policies framing researchers' duties with regard to incidental findings, this article also draws from Quebec's civil law--with its rich jurisprudence on clinician and researcher liability--as a case study to evaluate the potential legal implications associated with vaccinomics investigations. Given previous lessons learned from other data-intensive sciences, the education of clinician-researchers with regard to their roles, limitations, and legal obligations remains an important strategy to prevent potential legal complications and civil liability in vaccinomics research in the postgenomics era.     

A promiscuous DNA packaging machine from bacteriophage T4

Complex viruses are assembled from simple protein subunits by sequential and irreversible assembly. During genome packaging in bacteriophages, a powerful molecular motor assembles at the special portal vertex of an empty prohead to initiate packaging. The capsid expands after about 10%-25% of the genome is packaged. When the head is full, the motor cuts the concatemeric DNA and dissociates from the head. Conformational changes, particularly in the portal, are thought to drive these sequential transitions. We found that the phage T4 packaging machine is highly promiscuous, translocating DNA into finished phage heads as well as into proheads. Optical tweezers experiments show that single motors can force exogenous DNA into phage heads at the same rate as into proheads. Single molecule fluorescence measurements demonstrate that phage heads undergo repeated initiations, packaging multiple DNA molecules into the same head. These results suggest that the phage DNA packaging machine has unusual conformational plasticity, powering DNA into an apparently passive capsid receptacle, including the highly stable virus shell, until it is full. These features probably led to the evolution of viral genomes that fit capsid volume, a strikingly common phenomenon in double-stranded DNA viruses, and will potentially allow design of a novel class of nanocapsid delivery vehicles.     

Tetraploidization events by chromosome doubling of nucellar cells are frequent in apomictic citrus and are dependent on genotype and environment

Background and Aims

Polyploidy is a major component of plant evolution. The citrus gene pool is essentially diploid but tetraploid plants are frequently encountered in seedlings of diploid apomictic genotypes. The main objectives of the present study were to establish the origin of these tetraploid plants and to ascertain the importance of genotypic and environmental factors on tetraploid formation.

Methods

Tetraploid seedlings from 30 diploid apomictic genotypes were selected by flow cytometry and genotyped with 24 single sequence repeat (SSR) markers to analyse their genetic origin. Embryo rescue was used to grow all embryos contained in polyembryonic seeds of ‘Tardivo di Ciaculli’ mandarin, followed by characterization of the plantlets obtained by flow cytometry and SSR markers to accurately establish the rate of tetraploidization events and their potential tissue location. Inter-annual variations in tetraploid seedling rates were analysed for seven genotypes. Variation in tetraploid plantlet rates was analysed between different seedlings of the same genotype (‘Carrizo’ citrange; Citrus sinensis × Poncirus trifoliata) from seeds collected in different tropical, subtropical and Mediterranean countries.

Key Results

Tetraploid plants were obtained for all the studied diploid genotypes, except for four mandarins. All tetraploid plants were identical to their diploid maternal line for SSR markers and were not cytochimeric. Significant genotypic and environmental effects were observed, as well as negative correlation between mean temperature during the flowering period and tetraploidy seedling rates. The higher frequencies (20 %) of tetraploids were observed for citranges cultivated in the Mediterranean area.

Conclusions

Tetraploidization by chromosome doubling of nucellar cells are frequent events in apomictic citrus, and are affected by both genotypic and environmental factors. Colder conditions in marginal climatic areas appear to favour the expression of tetraploidization. Tetraploid genotypes arising from chromosome doubling of apomictic citrus are extensively being used as parents in breeding programmes to develop seedless triploid cultivars and have potential direct use as new rootstocks.     

Genomic databases access agreements: legal validity and possible sanctions

Large-scale, public genomic databases have greatly improved the capacity of researchers to do genomic research. In order to ensure that the scientific community uses data from these public resources properly, data access agreements have been developed to complement already existing legal and ethical norms. Sanctions to address cases of data misuse constitute an essential part of this compliance framework meant to protect stakeholders in genomic research. Yet very little research and community debate has been done on this most important topic. This paper presents a review of different sanctions that could be invoked in cases of non-compliance from data users. They have been identified through comprehensive research and analysis of over 450 documents (journal articles, policy, guidelines, access policies, etc.) related to this topic. Given the considerable impact on users of even the milder sanctions considered in our paper, it is essential that stakeholders strive to achieve the highest degree of standardization and transparency when designing controlled-access agreements. It is only fair, after all, that users be able to expect that the border between acceptable and unacceptable conduct is clearly delineated and predictable in controlled-access policies. This suggests the importance for researchers to undertake additional empirical studies on the clarity and accessibility of existing database access agreements and related policies in the near future.