Towards aspect-oriented functional--structural plant modelling

Background and Aims

Functional–structural plant models (FSPMs) are used to integrate knowledge and test hypotheses of plant behaviour, and to aid in the development of decision support systems. A significant amount of effort is being put into providing a sound methodology for building them. Standard techniques, such as procedural or object-oriented programming, are not suited for clearly separating aspects of plant function that criss-cross between different components of plant structure, which makes it difficult to reuse and share their implementations. The aim of this paper is to present an aspect-oriented programming approach that helps to overcome this difficulty.

Methods

The L-system-based plant modelling language L+C was used to develop an aspect-oriented approach to plant modelling based on multi-modules. Each element of the plant structure was represented by a sequence of L-system modules (rather than a single module), with each module representing an aspect of the element''s function. Separate sets of productions were used for modelling each aspect, with context-sensitive rules facilitated by local lists of modules to consider/ignore. Aspect weaving or communication between aspects was made possible through the use of pseudo-L-systems, where the strict-predecessor of a production rule was specified as a multi-module.

Key Results

The new approach was used to integrate previously modelled aspects of carbon dynamics, apical dominance and biomechanics with a model of a developing kiwifruit shoot. These aspects were specified independently and their implementation was based on source code provided by the original authors without major changes.

Conclusions

This new aspect-oriented approach to plant modelling is well suited for studying complex phenomena in plant science, because it can be used to integrate separate models of individual aspects of plant development and function, both previously constructed and new, into clearly organized, comprehensive FSPMs. In a future work, this approach could be further extended into an aspect-oriented programming language for FSPMs.     

Isolation and Purification of Drosophila Peripheral Neurons by Magnetic Bead Sorting

The Drosophila peripheral nervous system (PNS) is a powerful model for investigating the complex processes of neuronal development and dendrite morphogenesis at the functional and molecular levels. To aid in these analyses, we have developed a strategy for the isolation of a subclass of PNS neurons called dendritic arborization (da) neurons that have been widely used for studying dendrite morphogenesis^1,2. These neurons are very difficult to isolate as a pure population, due in part to their extremely low occurrence and their difficult-to-reach location below the tough chitinous larval cuticle. Our newly developed method overcomes these challenges, and is based on a fast and specific cell enrichment using antibody-coated magnetic beads. For our magnetic bead sorting studies, we have used age-matched third instar larvae expressing a mouse CD8 tagged GFP fusion protein (UAS-mCD8-GFP)³ under the control of either the class IV dendritic arborization (da) neuron-specific pickpocket (ppk)-GAL4 driver⁴ or the control of the pan-da neuron-specific GAL4^21-7 driver⁵. Although this protocol has been optimized for isolating PNS cells which are attached to the inner wall of the larval cuticle, by varying a few parameters, the same protocol could be used to isolate many different cell types attached to the cuticle at larval or pupal stages of development (e.g. epithelia, muscle, oenocytes etc.), or other cell types from larval organs depending upon the GAL4-specific driver expression pattern. The RNA isolated by this method is of high quality and can be readily used for downstream genomic analyses such as microarray gene expression profiling studies. This approach offers a powerful new tool to perform studies on isolated Drosophila dendritic arborization (da) neurons thereby providing novel insights into the molecular mechanisms underlying dendrite morphogenesis.Download video file.^{(149M, mp4)}     

Plasma Levels of Adiponectin,a Novel Adipocyte‐Derived Hormone,in Sleep Apnea**

Objective: Obstructive sleep apnea (OSA) is associated with obesity, sympathetic activation, systemic inflammation, and cardiovascular morbidity. Obesity, β‐adrenergic agonists, and inflammation are linked to decreased expression and/or secretion of an adipose tissue‐derived antiatherogenic hormone, adiponectin. The purpose of the study was to investigate whether OSA affected plasma levels of adiponectin, which might help explain OSA‐associated cardiovascular morbidity. Research Methods and Procedures: We randomly selected 68 otherwise healthy male subjects, either with moderate/severe OSA [apnea‐hypopnea index (AHI) ≥ 20; n = 35] or without OSA (AHI ≤ 5; n = 33). The diagnosis of OSA was made based on prospective full polysomnography. Adiponectin was measured before polysomnography between 8 and 10 PM . Results: AHI was higher in the OSA group (49.5 ± 4.4 vs. 2.9 ± 0.4 events/h; p < 0.001). OSA subjects were also more obese, with greater BMI (33 ± 1 vs. 30 ± 1; p = 0.016) and percentage body fat (29 ± 1% vs. 26 ± 1%; p = 0.030). Adiponectin levels were 7.67 ± 0.73 and 6.33 ± 0.51 μg/mL in the OSA and non‐OSA groups, respectively, and this difference was significant in covariate analysis (taking into account age, hemodynamic characteristics, measures of body fat, and OSA severity) (p = 0.009). After excluding from both groups the subjects with extreme BMI, such that the OSA and non‐OSA study cohorts had similar BMI and percentage body fat, subjects with OSA had significantly higher plasma adiponectin (8.49 ± 0.92 vs. 6.32 ± 0.55 μg/mL; p = 0.042), differences also evident in covariate analysis (p = 0.017). Discussion: Plasma adiponectin levels are elevated in otherwise healthy subjects with OSA. Therefore, low adiponectin is unlikely to explain the association between OSA and cardiovascular disease.     

QuickLIMS: facilitating the data management for DNA-microarray fabrication

SUMMARY: QuickLIMS is a Microsoft Access-based laboratory information and management system, capable of processing all information for microarray production. The program's operational flow is protocol-based, dynamically adapting to changes of the process. It interacts with the laboratory robot and with other database systems over the network, and it represents a complete solution for the management of the entire manufacturing process. AVAILABILITY AND SUPPLEMENTARY INFORMATION: http://www.dkfz-heidelberg.de/kompl_genome/Other/QuickLims/index.html     

Stream diatoms exhibit weak niche conservation along global environmental and climatic gradients

Niche conservatism (NC) describes the scenario in which species retain similar characteristics or traits over time and space, and thus has potentially important implications for understanding their biogeographic distributions. Evidence consistent with NC includes similar niche properties across geographically distant regions. We investigated whether NC was evident in stream diatom morphospecies by modeling species responses to environmental and climatic variables in a set of calibration sites (from the US) and then evaluated the models with test sets (from France, Finland, New Zealand, Antilles and La Réunion). We also examined whether diatom species showed congruency in environmental niche optima and niche breadths between the study regions, and whether species occupancy and functional traits influenced the observed patterns. We used boosted regression tree models with local environmental variables and climatic variables as predictors. We detected low NC in both environmental and climate models and a lack of consistent differences in NC between widely distributed and regionally rare species and among functional groups. For all species, diatom environmental and climatic optima varied clearly between the regions but showed some positive relationships especially for pH and total phosphorus. Diatom niche breadths were only weakly correlated between the US and the other regions. We demonstrated that diatoms showed overall relatively little NC globally, and NC was especially low for climatic variables. Collectively, these findings suggest that there may exist locally adapted lineages within the diatom morphospecies or diatoms possess some adaptation potential for differences in temperature. We argue that in diatoms, environmental and especially climate models may not be transferrable in space globally but need regional diatom data for calibration because species niches seem to differ among geographical regions.     

Reconstitution of human atlastin fusion activity reveals autoinhibition by the C terminus

ER network formation depends on membrane fusion by the atlastin (ATL) GTPase. In humans, three paralogs are differentially expressed with divergent N- and C-terminal extensions, but their respective roles remain unknown. This is partly because, unlike Drosophila ATL, the fusion activity of human ATLs has not been reconstituted. Here, we report successful reconstitution of fusion activity by the human ATLs. Unexpectedly, the major splice isoforms of ATL1 and ATL2 are each autoinhibited, albeit to differing degrees. For the more strongly inhibited ATL2, autoinhibition mapped to a C-terminal α-helix is predicted to be continuous with an amphipathic helix required for fusion. Charge reversal of residues in the inhibitory domain strongly activated its fusion activity, and overexpression of this disinhibited version caused ER collapse. Neurons express an ATL2 splice isoform whose sequence differs in the inhibitory domain, and this form showed full fusion activity. These findings reveal autoinhibition and alternate splicing as regulators of atlastin-mediated ER fusion.     

Altered Levels of Mitochondrial DNA Are Associated with Female Age,Aneuploidy, and Provide an Independent Measure of Embryonic Implantation Potential

Mitochondria play a vital role in embryo development. They are the principal site of energy production and have various other critical cellular functions. Despite the importance of this organelle, little is known about the extent of variation in mitochondrial DNA (mtDNA) between individual human embryos prior to implantation. This study investigated the biological and clinical relevance of the quantity of mtDNA in 379 embryos. These were examined via a combination of microarray comparative genomic hybridisation (aCGH), quantitative PCR and next generation sequencing (NGS), providing information on chromosomal status, amount of mtDNA, and presence of mutations in the mitochondrial genome. The quantity of mtDNA was significantly higher in embryos from older women (P=0.003). Additionally, mtDNA levels were elevated in aneuploid embryos, independent of age (P=0.025). Assessment of clinical outcomes after transfer of euploid embryos to the uterus revealed that blastocysts that successfully implanted tended to contain lower mtDNA quantities than those failing to implant (P=0.007). Importantly, an mtDNA quantity threshold was established, above which implantation was never observed. Subsequently, the predictive value of this threshold was confirmed in an independent blinded prospective study, indicating that abnormal mtDNA levels are present in 30% of non-implanting euploid embryos, but are not seen in embryos forming a viable pregnancy. NGS did not reveal any increase in mutation in blastocysts with elevated mtDNA levels. The results of this study suggest that increased mtDNA may be related to elevated metabolism and are associated with reduced viability, a possibility consistent with the ‘quiet embryo’ hypothesis. Importantly, the findings suggest a potential role for mitochondria in female reproductive aging and the genesis of aneuploidy. Of clinical significance, we propose that mtDNA content represents a novel biomarker with potential value for in vitro fertilisation (IVF) treatment, revealing chromosomally normal blastocysts incapable of producing a viable pregnancy.     

Local–regional diversity relationship varies with spatial scale in lotic diatoms

Aim Ecologists have shown increasing interest in the relative roles of local and regional factors in structuring biotic communities. One approach to studying this is to examine the relationship between local species richness (LSR) and regional species richness (RSR). We examined the LSR–RSR relationship in stream diatoms, using two data sets that varied in spatial extent. At broad spatial extent ranging across drainage systems, we expected climatic and dispersal‐related factors to constrain LSR, thus resulting in a linear LSR–RSR relationship. However, at small spatial scales dispersal across sites should be unconstrained, resulting in strong local interactions and a weak or asymptotic LSR–RSR relationship. Location Boreal streams in Finland. Methods For data set 1, we sampled 15 stream riffles (localities) in each of eight drainage systems (regions), with the latitudinal gradient between the southernmost and northernmost sites being almost 1100 km. For data set 2, a locality for estimating LSR was a single stone, and each riffle represented a region for estimating RSR. We sampled 20 stones in each of eight riffles. We used linear regressions to examine the relationship between LSR and RSR across regions. We used both observed richness values, as well as values estimated with the Chao1 estimator. Results We found a relatively strong linear relationship between the Chao1‐estimated mean LSR and RSR (R² = 0.654, P = 0.015) across drainage systems. The slope of the regression was 0.643 and it did not differ from 1.0, thus indicating linearity. At the riffle scale, however, LSR and RSR were not linearly related, and the slope of the regression (0.039) differed significantly from 1.0, indicating curvilinearity. Main conclusions These results suggest that the relationship between mean LSR and RSR varies across spatial scales in diatoms – from significantly linear at large scales to curvilinear at small scales. These plots imply strong regional enrichment in stream diatoms across drainage systems. Their diversity is thus determined largely by the composition of the regional species pool, as also in many macroorganisms. In contrast, at small spatial scales the LSR–RSR relationship implied a hard limit to local diversity, reflecting the primacy of local processes.