Artifacts in the assay of maize leaf phosphoenolpyruvate carboxylase activity due to its instability

When the assay of maize leaf phosphoenolpyruvate carboxylase (EC 4.1.1.31) activity is started with phosphoenolpyruvate, much lower reaction rates are obtained as compared to the enzyme-initiated reaction. The difference is due to the lability of the dilute enzyme in the absence of its substrate and is increased with incubation time in the absence of substrate or stabilizers. The activation of the enzyme by glucose-6-phosphate is overestimated with the substrate-initiated assay since a part of the apparent activation is due to stabilization of the enzymic activity by this effector during the minus-substrate preincubation. In contrast, the inhibitory effect of malate is underestimated when the reaction is started with the substrate. The enzyme-initiated assay is recommended provided that the necessary corrections for apparent activity in the absence of substrate and for inactivation during the assay at low substrate levels are made.Abbreviations DTT dithiothreitol - G-6-P glucose-6-phosphate - MDH malate dehydrogenase - PEP phosphoenolpyruvate - PEPCase phosphoenolpyruvate carboxylase - PVP polyvinylpyrrolidone     

Dark-to-light transition in <Emphasis Type="Italic">Synechococcus</Emphasis> sp. PCC 7942 cells studied by fluorescence kinetics assesses plastoquinone redox poise in the dark and photosystem II fluorescence component and dynamics during state 2 to state 1 transition

We investigated the dark-to-light transition in Synechococcus sp. PCC 7942 cells by a detailed analysis of fluorescence transients induced by strong red light. The transients, recorded with high data-acquisition, revealed all the steps of the fast (OJIP; 10⁻⁵–1 s) and slow phase (PSM(T); 1–10³ s), kinetically distinguished with precision. Focusing on the OJIP-rise, we show, for the first time, how the variable to initial fluorescence ratio and the relative height of J-level can serve as indexes of the plastoquinone redox poise and the established state in the dark; hence, differences among cyanobacteria can be recognised in a simple way. Applying intermittent illumination (20-s light pulses separated by 10-s dark intervals) to induce dark-to-light transition and analysing the individual transients, we establish a method by which we determine the fluorescence component not originating from photosystem (PS) II and we assess PSII dynamics during state 2 to state 1 transition. The development of photochemical and non-photochemical quenching is also discussed, as well as evidences favouring the mobile antenna model.     

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8,736 out of all 16,453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into subclasses using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.     

Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood

We present an evolutionary placement algorithm (EPA) and a Web server for the rapid assignment of sequence fragments (short reads) to edges of a given phylogenetic tree under the maximum-likelihood model. The accuracy of the algorithm is evaluated on several real-world data sets and compared with placement by pair-wise sequence comparison, using edit distances and BLAST. We introduce a slow and accurate as well as a fast and less accurate placement algorithm. For the slow algorithm, we develop additional heuristic techniques that yield almost the same run times as the fast version with only a small loss of accuracy. When those additional heuristics are employed, the run time of the more accurate algorithm is comparable with that of a simple BLAST search for data sets with a high number of short query sequences. Moreover, the accuracy of the EPA is significantly higher, in particular when the sample of taxa in the reference topology is sparse or inadequate. Our algorithm, which has been integrated into RAxML, therefore provides an equally fast but more accurate alternative to BLAST for tree-based inference of the evolutionary origin and composition of short sequence reads. We are also actively developing a Web server that offers a freely available service for computing read placements on trees using the EPA.     

Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes

Background  

An adaptive coarse-grained (kinetic) Monte Carlo (ACGMC) simulation framework is applied to reaction and diffusion dynamics in inhomogeneous domains. The presented model is relevant to the diffusion and dimerization dynamics of epidermal growth factor receptor (EGFR) in the presence of plasma membrane heterogeneity and specifically receptor clustering. We perform simulations representing EGFR cluster dissipation in heterogeneous plasma membranes consisting of higher density clusters of receptors surrounded by low population areas using the ACGMC method. We further investigate the effect of key parameters on the cluster lifetime.     

Beneficial effects of enhanced UV-B radiation under field conditions: improvement of needle water relations and survival capacity of Pinus pinea L. seedlings during the dry Mediterranean summer

The possible mechanism(s) by which supplemental UV-B radiation alleviates the adverse effects of summer drought in Mediterranean pines (Petropoulou et al. 1995) were investigated with seedlings of Pinus pinea. Plants received ambient or ambient plus supplemental UV-B radiation (biologically equivalent to a 15% ozone depletion over Patras, 38.3° N, 29.1° E) and natural precipitation or additional irrigation. Treatments started on 1 February, 1994 and lasted up to the end of the dry period (29 September). In well-watered plants, UV-B radiation had no influence on photosystem II photochemical efficiency and biomass accumulation. Water stressed plants suffered from needle loss and reduced photosystem II photochemical efficiency during the summer. These symptoms, however, were less pronounced in plants receiving supplemental UV-B radiation, resulting in higher total biomass at plant harvest. Laboratory tests showed that enhanced UV-B radiation did not improve the tolerance of photosystem II against drought, high light, high temperature and oxidative stress. Enhanced UV-B radiation, however, improved the water economy of water stressed plants, as judged by measurements of needle relative water content. In addition, it caused an almost two-fold increase of cuticle thickness. No such UV-B radiation effects were observed in well-watered pines. The results indicate that the combination of water stress and UV-B radiation may trigger specific responses, enabling the plants to avoid excessive water loss and, thereby, maintain a more efficient photosynthetic apparatus during the summer. The extent of this apparently positive UV-B radiation effect would depend on the amount of summer precipitation. Abbreviations: DW – dry weight, F_v/F_m – ratio of variable to maximum fluorescence, A ₃₀₀ – absorbance at 300 nm, PAR – photosynthetically active radiation, PS II – photosystem II, RWC – relative water content, TCA – trichloroacetic acid, UV-B_BE – biologically effective ultraviolet-B radiation     

A mathematical and computational approach for integrating the major sources of cell population heterogeneity

Several approaches have been used in the past to model heterogeneity in bacterial cell populations, with each approach focusing on different source(s) of heterogeneity. However, a holistic approach that integrates all the major sources into a comprehensive framework applicable to cell populations is still lacking.In this work we present the mathematical formulation of a cell population master equation (CPME) that describes cell population dynamics and takes into account the major sources of heterogeneity, namely stochasticity in reaction, DNA-duplication, and division, as well as the random partitioning of species contents into the two daughter cells. The formulation also takes into account cell growth and respects the discrete nature of the molecular contents and cell numbers. We further develop a Monte Carlo algorithm for the simulation of the stochastic processes considered here. To benchmark our new framework, we first use it to quantify the effect of each source of heterogeneity on the intrinsic and the extrinsic phenotypic variability for the well-known two-promoter system used experimentally by Elowitz et al. (2002). We finally apply our framework to a more complicated system and demonstrate how the interplay between noisy gene expression and growth inhibition due to protein accumulation at the single cell level can result in complex behavior at the cell population level.The generality of our framework makes it suitable for studying a vast array of artificial and natural genetic networks. Using our Monte Carlo algorithm, cell population distributions can be predicted for the genetic architecture of interest, thereby quantifying the effect of stochasticity in intracellular reactions or the variability in the rate of physiological processes such as growth and division. Such in silico experiments can give insight into the behavior of cell populations and reveal the major sources contributing to cell population heterogeneity.