Rubisco evolution in C4 eudicots: an analysis of Amaranthaceae sensu lato

BACKGROUND Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyses the key reaction in the photosynthetic assimilation of CO₂. In C₄ plants CO₂ is supplied to Rubisco by an auxiliary CO₂-concentrating pathway that helps to maximize the carboxylase activity of the enzyme while suppressing its oxygenase activity. As a consequence, C₄ Rubisco exhibits a higher maximum velocity but lower substrate specificity compared with the C₃ enzyme. Specific amino-acids in Rubisco are associated with C₄ photosynthesis in monocots, but it is not known whether selection has acted on Rubisco in a similar way in eudicots. METHODOLOGY/PRINCIPAL FINDINGS We investigated Rubisco evolution in Amaranthaceae sensu lato (including Chenopodiaceae), the third-largest family of C₄ plants, using phylogeny-based maximum likelihood and Bayesian methods to detect Darwinian selection on the chloroplast rbcL gene in a sample of 179 species. Two Rubisco residues, 281 and 309, were found to be under positive selection in C₄ Amaranthaceae with multiple parallel replacements of alanine by serine at position 281 and methionine by isoleucine at position 309. Remarkably, both amino-acids have been detected in other C₄ plant groups, such as C₄ monocots, illustrating a striking parallelism in molecular evolution. CONCLUSIONS/SIGNIFICANCE Our findings illustrate how simple genetic changes can contribute to the evolution of photosynthesis and strengthen the hypothesis that parallel amino-acid replacements are associated with adaptive changes in Rubisco.This research was funded by NERC (http://www.nerc.ac.uk/; grant number NE/H007741/1)

Observable effects caused by vacuum pair creation in the field of high-power optical lasers

We consider the possibility of an experimental proof of vacuum e+e- pair creation in the focus of two counter-propagating optical laser beams with an intensity of the order of 10^20 - 10^22 W/cm^2. Our approach is based on the collisionless kinetic equation for the distribution function of the e+e- pairs with the source term for particle production. As a possible experimental signal of vacuum pair production we consider the refraction of a high-frequency probe laser beam by the produced e+e- plasma to be observed by an interference filter. The generation of higher harmonics of the laser frequency in the self-consistent electric field is also investigated.Comment: 7 pages, 7 figures; typos corrected, Eq.(16) corrected, reference adde

Аналіз застосовності комерційно доступного хімічного простору для використання у 19F ЯМР FAXS методі на прикладі НВП «Єнамін»

Aim. To analyze commercially available fluorine containing compounds for the possibility of their use in the 19F NMR FAXS method.Materials and methods. The selection of fluorine-containing fragments for the study was performed using 3.9 million instock screening compounds and 248,000 in-stock building-blocks from Enamine Ltd library. The selection and classification of the compounds was carried out using the DataWarrior and KNIME software. The Fluorinated Fragments library of Enamine Ltd. containing 6377 compounds, was also analyzed. To analyze the abovementioned sets of substances, the multistep workflows specially designed were used.Results and discussion. As a result of applying the workflow developed to the compound sets (both screening compounds and building blocks), 13 800 compounds were selected and further classified according to the presence of one out of 12 fluorine-containing groups. The Fluorinated Fragments library was also subjected to a similar workflow. For the latter, 8 out of 12 fluorine-containing groups were identified. Additionally, experimental 19F NMR chemical shift values for Fluorinated Fragments library compounds spectra were analyzed. It has been found that some structural classes have areas of chemical shifts intersection. On the other hand, the ranges from –40 to –60 ppm and beyond –160 ppm are free from any group of compounds from the library analyzed.Conclusions. The analysis has shown that commercially available fluorine-containing fragments do not satisfy the needs of the 19F NMR FAXS method, and further expansion of the chemical space of fluorine-containing compounds by increasing their diversity is required.Мета. Проаналізувати комерційно доступні флуоровмісні сполуки на можливість їх застосування в конкурентному скринінгу за допомогою 19F ЯМР FAXS методу.Матеріали та методи. Відбір флуоровмісних фрагментів для дослідження проводили з використанням наявних на складі компанії ТОВ «НВП «Єнамін» 3,9 млн скринінгових сполук та 248000 будівельних блоків. Відбір та розподіл сполук по групах виконували за допомогою програм DataWarrior та KNIME. Проаналізували бібліотеку флуорованих фрагментів ТОВ «НВП «Єнамін», що містить 6377 сполук. Для аналізу вищезазначених наборів речовин використовували спеціально розроблені багатоступеневі алгоритми.Результати та їх обговорення. У результаті застосування розробленого алгоритму до скринінгових сполук та будівельних блоків відібрано 13800 представників, які додатково класифіковано за наявністю однієї з 12 флуоровмісних груп. Бібліотеку флуорованих фрагментів також піддано подібній процедурі. Для останньої групи досліджуваних сполук ідентифіковано наявність 8 з 12 флуоровмісних фрагментів. Крім того, проаналізовано експериментальні значення хімічного зсуву, отримані із 19F ЯМР спектрів бібліотеки флуорованих фрагментів. З’ясовано, що деякі структурні класи мають зони перетину хімічних зсувів. З іншого боку, у діапазонах від –40 до –60 м.д. і більше –160 м.д. не представлено жодної сполуки з аналізованої бібліотеки.Висновки. Аналіз засвідчив, що наявні комерційно доступні флуоровмісні фрагменти не задовольняють потреби 19F NMR FAXS методу, а тому необхідно розширювати хімічний простір флуоровмісних сполук шляхом збільшення їх різноманіття

Molecular Adaptation during Adaptive Radiation in the Hawaiian Endemic Genus Schiedea

BACKGROUND: “Explosive” adaptive radiations on islands remain one of the most puzzling evolutionary phenomena. The rate of phenotypic and ecological adaptations is extremely fast during such events, suggesting that many genes may be under fairly strong selection. However, no evidence for adaptation at the level of protein coding genes was found, so it has been suggested that selection may work mainly on regulatory elements. Here we report the first evidence that positive selection does operate at the level of protein coding genes during rapid adaptive radiations. We studied molecular adaptation in Hawaiian endemic plant genus Schiedea (Caryophyllaceae), which includes closely related species with a striking range of morphological and ecological forms, varying from rainforest vines to woody shrubs growing in desert-like conditions on cliffs. Given the remarkable difference in photosynthetic performance between Schiedea species from different habitats, we focused on the “photosynthetic” Rubisco enzyme, the efficiency of which is known to be a limiting step in plant photosynthesis. RESULTS: We demonstrate that the chloroplast rbcL gene, encoding the large subunit of Rubisco enzyme, evolved under strong positive selection in Schiedea. Adaptive amino acid changes occurred in functionally important regions of Rubisco that interact with Rubisco activase, a chaperone which promotes and maintains the catalytic activity of Rubisco. Interestingly, positive selection acting on the rbcL might have caused favorable cytotypes to spread across several Schiedea species. SIGNIFICANCE: We report the first evidence for adaptive changes at the DNA and protein sequence level that may have been associated with the evolution of photosynthetic performance and colonization of new habitats during a recent adaptive radiation in an island plant genus. This illustrates how small changes at the molecular level may change ecological species performance and helps us to understand the molecular bases of extremely fast rate of adaptation during island adaptive radiations

Widespread positive selection in the photosynthetic Rubisco enzyme

Background: Rubisco enzyme catalyzes the first step in net photosynthetic CO2 assimilation and photorespiratory carbon oxidation and is responsible for almost all carbon fixation on Earth. The large subunit of Rubisco is encoded by the chloroplast rbcL gene, which is widely used for reconstruction of plant phylogenies due to its conservative nature. Plant systematicists have mainly used rbcL paying little attention to its function, and the question whether it evolves under Darwinian selection has received little attention. The purpose of our study was to evaluate how common is positive selection in Rubisco among the phototrophs and where in the Rubisco structure does positive selection occur. Results: We searched for positive selection in rbcL sequences from over 3000 species representing all lineages of green plants and some lineages of other phototrophs, such as brown and red algae, diatoms, euglenids and cyanobacteria. Our molecular phylogenetic analysis found the presence of positive selection in rbcL of most analyzed land plants, but not in algae and cyanobacteria. The mapping of the positively selected residues on the Rubisco tertiary structure revealed that they are located in regions important for dimer-dimer, intradimer, large subunit-small subunit and Rubisco-Rubisco activase interactions, and that some of the positively selected residues are close to the active site. Conclusion: Our results demonstrate that despite its conservative nature, Rubisco evolves under positive selection in most lineages of land plants, and after billions of years of evolution Darwinian selection still fine-tunes its performance. Widespread positive selection in rbcL has to be taken into account when this gene is used for phylogenetic reconstructions. </p

FROM THE DEPARTMENT OF GEOPHYSICS TO THE FACULTY OF GEOPHYSICS

By the mid-1930's, in the Urals, a scientific-pedagogical geophysical school was formed, the basis of which was the Department of Geophysics of the Sverdlovsk Mining Institute. The department has been developed significantly from the point of view of science and personnel during the Great Patriotic War: its staff has defended seven Ph.D. theses and one doctorate thesis; in 1942 and 1945, the members of the department were counterparts for the Stalin Prize. Therefore, it is natural that in September 1951, a geophysical faculty was formed on the basis of the department. The first dean of the faculty was the head of the department of geophysics, a gifted apprentice of P.K. Sobolevsky, N. A. Ivanov