Plantecophys - An R Package for Analysing and Modelling Leaf Gas Exchange Data

Here I present the R package ''plantecophys'', a toolkit to analyse and model leaf gas exchange data. Measurements of leaf photosynthesis and transpiration are routinely collected with portable gas exchange instruments, and analysed with a few key models. These models include the Farquhar-von Caemmerer-Berry (FvCB) model of leaf photosynthesis, the Ball-Berry models of stomatal conductance, and the coupled leaf gas exchange model which combines the supply and demand functions for CO₂ in the leaf. The ''plantecophys'' R package includes functions for fitting these models to measurements, as well as simulating from the fitted models to aid in interpreting experimental data. Here I describe the functionality and implementation of the new package, and give some examples of its use. I briefly describe functions for fitting the FvCB model of photosynthesis to measurements of photosynthesis-CO₂ response curves (''A-C_i curves''), fitting Ball-Berry type models, modelling C3 photosynthesis with the coupled photosynthesis-stomatal conductance model, modelling C4 photosynthesis, numerical solution of optimal stomatal behaviour, and energy balance calculations using the Penman-Monteith equation. This open-source package makes technically challenging calculations easily accessible for many users and is freely available on CRAN.     

Plant evolution: AGC kinases tell the auxin tale

The signaling molecule auxin is a central regulator of plant development, which instructs tissue and organ patterning, and couples environmental stimuli to developmental responses. Here, we discuss the function of PINOID (PID) and the phototropins, members of the plant specific AGCVIII protein kinases, and their role in triggering and regulating development by controlling PIN-FORMED (PIN) auxin transporter-generated auxin gradients and maxima. We propose that the AGCVIII kinase gene family evolved from an ancestral phototropin gene, and that the co-evolution of PID-like and PIN gene families marks the transition of plants from water to land. We hypothesize that the PID-like kinases function in parallel to, or downstream of, the phototropins to orient plant development by establishing the direction of polar auxin transport.     

Using models to guide field experiments: a priori predictions for the CO2 response of a nutrient‐ and water‐limited native Eucalypt woodland

The response of terrestrial ecosystems to rising atmospheric CO₂ concentration (C_a), particularly under nutrient‐limited conditions, is a major uncertainty in Earth System models. The Eucalyptus Free‐Air CO₂ Enrichment (EucFACE) experiment, recently established in a nutrient‐ and water‐limited woodland presents a unique opportunity to address this uncertainty, but can best do so if key model uncertainties have been identified in advance. We applied seven vegetation models, which have previously been comprehensively assessed against earlier forest FACE experiments, to simulate a priori possible outcomes from EucFACE. Our goals were to provide quantitative projections against which to evaluate data as they are collected, and to identify key measurements that should be made in the experiment to allow discrimination among alternative model assumptions in a postexperiment model intercomparison. Simulated responses of annual net primary productivity (NPP) to elevated C_a ranged from 0.5 to 25% across models. The simulated reduction of NPP during a low‐rainfall year also varied widely, from 24 to 70%. Key processes where assumptions caused disagreement among models included nutrient limitations to growth; feedbacks to nutrient uptake; autotrophic respiration; and the impact of low soil moisture availability on plant processes. Knowledge of the causes of variation among models is now guiding data collection in the experiment, with the expectation that the experimental data can optimally inform future model improvements.     

Prevalence of c-KIT Mutations in Gonadoblastoma and Dysgerminomas of Patients with Disorders of Sex Development (DSD) and Ovarian Dysgerminomas

Activating c-KIT mutations (exons 11 and 17) are found in 10-40% of testicular seminomas, the majority being missense point mutations (codon 816). Malignant ovarian dysgerminomas represent ～3% of all ovarian cancers in Western countries, resembling testicular seminomas, regarding chromosomal aberrations and c-KIT mutations. DSD patients with specific Y-sequences have an increased risk for Type II Germ Cell Tumor/Cancer, with gonadoblastoma as precursor progressing to dysgerminoma. Here we present analysis of c-KIT exon 8, 9, 11, 13 and 17, and PDGFRA exon 12, 14 and 18 by conventional sequencing together with mutational analysis of c-KIT codon 816 by a sensitive and specific LightCycler melting curve analysis, confirmed by sequencing. The results are combined with data on TSPY and OCT3/4 expression in a series of 16 DSD patients presenting with gonadoblastoma and dysgerminoma and 15 patients presenting pure ovarian dysgerminomas without DSD. c-KIT codon 816 mutations were detected in five out of the total of 31 cases (all found in pure ovarian dysgerminomas). A synonymous SNP (rs 5578615) was detected in two patients, one DSD patient (with bilateral disease) and one patient with dysgerminoma. Next to these, three codon N822K mutations were detected in the group of 15 pure ovarian dysgerminomas. In total activating c-KIT mutations were found in 53% of ovarian dysgerminomas without DSD. In the group of 16 DSD cases a N505I and D820E mutation was found in a single tumor of a patient with gonadoblastoma and dysgerminoma. No PDGFRA mutations were found. Positive OCT3/4 staining was present in all gonadoblastomas and dysgerminomas investigated, TSPY expression was only seen in the gonadoblastoma/dysgerminoma lesions of the 16 DSD patients. This data supports the existence of two distinct but parallel pathways in the development of dysgerminoma, in which mutational status of c-KIT might parallel the presence of TSPY.     

Evolution of blind beetles in isolated aquifers: a test of alternative modes of speciation

Evidence is growing that not only allopatric but also sympatric speciation can be important in the evolution of species. Sympatric speciation has most convincingly been demonstrated in laboratory experiments with bacteria, but field-based evidence is limited to a few cases. The recently discovered plethora of subterranean diving beetle species in isolated aquifers in the arid interior of Australia offers a unique opportunity to evaluate alternative modes of speciation. This naturally replicated evolutionary experiment started 10-5 million years ago, when climate change forced the surface species to occupy geographically isolated subterranean aquifers. Using phylogenetic analysis, we determine the frequency of aquifers containing closely related sister species. By comparing observed frequencies with predictions from different statistical models, we show that it is very unlikely that the high number of sympatrically occurring sister species can be explained by a combination of allopatric evolution and repeated colonisations alone. Thus, diversification has occurred within the aquifers and likely involved sympatric, parapatric and/or microallopatric speciation.     

3DM: Systematic analysis of heterogeneous superfamily data to discover protein functionalities

Ten years of experience with molecular class–specific information systems (MCSIS) such as with the hand‐curated G protein–coupled receptor database (GPCRDB) or the semiautomatically generated nuclear receptor database has made clear that a wide variety of questions can be answered when protein‐related data from many different origins can be flexibly combined. MCSISes revolve around a multiple sequence alignment (MSA) that includes “all” available sequences from the entire superfamily, and it has been shown at many occasions that the quality of these alignments is the most crucial aspect of the MCSIS approach. We describe here a system called 3DM that can automatically build an entire MCSIS. 3DM bases the MSA on a multiple structure alignment, which implies that the availability of a large number of superfamily members with a known three‐dimensional structure is a requirement for 3DM to succeed well. Thirteen MCSISes were constructed and placed on the Internet for examination. These systems have been instrumental in a large series of research projects related to enzyme activity or the understanding and engineering of specificity, protein stability engineering, DNA‐diagnostics, drug design, and so forth. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Postdelivery changes in maternal and infant erythrocyte fatty acids in 3 populations differing in fresh water fish intakes

Introduction

Long-chain polyunsaturated (LCP) fatty acids (FA) are important during infant development. Mother-to-infant FA-transport occurs at the expense of the maternal status. Maternal and infant FA-status change rapidly after delivery.

Methods

Comparison of maternal (mRBC) and infant erythrocyte (iRBC)-FA-profiles at delivery and after 3 months exclusive breastfeeding in relation to freshwater-fish intakes. Approximation of de-novo-lipogenesis (DNL), stearoyl-CoA-desaturase (SCD), elongation-of-very-long-chain-FA-family-member-6 (Elovl-6), delta-5-desaturase (D5D) and delta-6-desaturase (D6D)-enzymatic activities from their product/essential-FA and product/substrate-ratios.

Results and discussion

Increasing iRBC-14:0 derived from mammary-gland DNL. Decreasing mRBC-ω9, but increasing iRBC-ω9, suggest high ω9-FA-transfer via breastmilk. Decreasing (m+i)RBC-16:0, DNL- and SCD-activities, but increasing (m+i)RBC-18:0 and Elovl-6-activity suggest more pronounced postpartum decreases in DNL- and SCD-activities, compared to Elovl-6-activity. Increasing (m+i)RBC-18:3ω3, 20:5ω3, 22:5ω3, 18:2ω6, mRBC-20:4ω6 and (m+i)D5D-activity, but decreasing mRBC-22:6ω3 and (m+i)D6D-activity and dose-dependent changes in iRBC-22:6ω3 confirm that D6D-activity is rate-limiting and 22:6ω3 is important during lactation. Fish-intake related magnitudes of postpartum FA-changes suggest that LCPω3 influence DNL-, SCD- and desaturase-activities.     

Effect of metal Ions (Ni<Superscript>2+</Superscript>, Cu<Superscript>2+</Superscript> and Zn<Superscript>2+</Superscript>) and water coordination on the structure of L-phenylalanine,L-tyrosine,L-tryptophan and their zwitterionic forms

Methods of quantum chemistry have been applied to double-charged complexes involving the transition metals Ni²⁺, Cu²⁺ and Zn²⁺ with the aromatic amino acids (AAA) phenylalanine, tyrosine and tryptophan. The effect of hydration on the relative stability and geometry of the individual species studied has been evaluated within the supermolecule approach. The interaction enthalpies, entropies and Gibbs energies of nine complexes Phe•M, Tyr•M, Trp•M, (M = Ni²⁺, Cu²⁺ and Zn²⁺) were determined at the Becke3LYP density functional level of theory. Of the transition metals studied the bivalent copper cation forms the strongest complexes with AAAs. For Ni²⁺and Cu²⁺ the most stable species are the NO coordinated cations in the AAA metal complexes, Zn²⁺cation prefers a binding to the aromatic part of the AAA (complex II). Some complexes energetically unfavored in the gas-phase are stabilized upon microsolvation.