Effect of exogenous cytokinins,auxins and adenine on cytokinin <Emphasis Type="Italic">N</Emphasis>-glucosylation and cytokinin oxidase/dehydrogenase activity in de-rooted radish seedlings

The role of cytokinin N-glucosylation and degradation by cytokinin oxidase/dehydrogenase (CKX, EC 1.5.99.12) in response to application of exogenous auxins (2,4-dichlorophenoxyacetic acid [2,4-D] and -naphthaleneacetic acid [NAA]) and cytokinins (N ⁶-benzyladenine [BA] and trans-zeatin [Z]) was investigated in de-rooted seedlings of Raphanus sativus L. cv. Rampouch. Both auxins applied for 24 h at 1 and 10 M concentration increased N-glucosylation of exogenously applied [³H]dihydrozeatin (DHZ) by up to 20%. The level of endogenous 7N-glucosides (of Z, isopentenyladenine [iP] and DHZ) was increased by 2,4-D and NAA at 10 M concentration by 28 and 23%, respectively, the level of Z being decreased by 90 and 59%, respectively. 2,4-D and NAA suppressed CKX activity ca. by half. Exogenous cytokinins Z and BA applied at 1 and 10 M concentration stimulated 7N-glucosylation of [³H]DHZ (by up to 40%). BA both at 1 and 10 M, increased the level of endogenous Z by up to 35% and that of 7N-glucosides by up to 27%. BA application also strongly stimulated CKX activity (by up to 180%). Feeding with 1 and 10 M Z resulted in ca. 100-fold and 2000-fold increase of Z level, respectively. The main metabolite, Z7G, was increased ca. 6-fold and 60-fold, respectively. Levels of Z 9-glucoside (Z9G), trans-zeatin riboside (ZR) and Z O-glucoside (ZOG) were elevated to lesser extent. As compared to BA, Z had only negligible effect on CKX activity. Adenine (1–500 M) was preferentially 7N-glucosylated inhibiting competitively 7N-glucosylation of [³H]DHZ. At high concentrations (100–500 M) it increased endogenous levels of active cytokinins, especially of Z, however, it had no effect on CKX activity. Cytokinin N-glucosylation proved to be involved in down-regulation of active cytokinins in response to auxin and in the re-establishment of cytokinin homeostasis following application of exogenous cytokinins.     

Bio-steps beyond Turing

Are there 'biologically computing agents' capable to compute Turing uncomputable functions? It is perhaps tempting to dismiss this question with a negative answer. Quite the opposite, for the first time in the literature on molecular computing we contend that the answer is not theoretically negative. Our results will be formulated in the language of membrane computing (P systems). Some mathematical results presented here are interesting in themselves. In contrast with most speed-up methods which are based on non-determinism, our results rest upon some universality results proved for deterministic P systems. These results will be used for building "accelerated P systems". In contrast with the case of Turing machines, acceleration is a part of the hardware (not a quality of the environment) and it is realised either by decreasing the size of "reactors" or by speeding-up the communication channels. Consequently, two acceleration postulates of biological inspiration are introduced; each of them poses specific questions to biology. Finally, in a more speculative part of the paper, we will deal with Turing non-computability activity of the brain and possible forms of (extraterrestrial) intelligence.     

A formal language-based approach in biology

This paper presents an overview of computational biology approaches and surveys some of the natural computing models using, in both cases, a formal language-based approach.     

Three‐dimensional correlative single‐cell imaging utilizing fluorescence and refractive index tomography

Cells alter the path of light, a fact that leads to well‐known aberrations in single cell or tissue imaging. Optical diffraction tomography (ODT) measures the biophysical property that causes these aberrations, the refractive index (RI). ODT is complementary to fluorescence imaging and does not require any markers. The present study introduces RI and fluorescence tomography with optofluidic rotation (RAFTOR) of suspended cells, facilitating the segmentation of the 3D‐correlated RI and fluorescence data for a quantitative interpretation of the nuclear RI. The technique is validated with cell phantoms and used to confirm a lower nuclear RI for HL60 cells. Furthermore, the nuclear inversion of adult mouse photoreceptor cells is observed in the RI distribution. The applications shown confirm predictions of previous studies and illustrate the potential of RAFTOR to improve our understanding of cells and tissues.      

Effect of Cytokinin and Auxin Treatments on Morphogenesis,Terpenoid Biosynthesis,Photosystem Structural Organization,and Endogenous Isoprenoid Cytokinin Profile in <Emphasis Type="Italic">Artemisia alba</Emphasis> Turra In Vitro

Developmental pattern modification in essential oil bearing Artemisia alba Turra was obtained by exogenous plant growth regulator (PGRs) treatments in vitro. Enhanced rooting (in PGR-free and auxin-treated plants) led to elevation of the monoterpenoid/sesquiterpenoid ratio in the essential oils of aerials. On the contrary, root inhibition and intensive callusogenesis [combined cytokinin (CK) and auxin treatments] reduced this ratio more than twice, significantly enhancing sesquiterpenoid production. Both morphogenic types displayed sesquiterpenoid domination in the underground tissues, which however differed qualitatively from the sesquiterpenoids of the aerials, excluding the hypothesis of their shoot-to-root translocation and implying the possible role of another signaling factor, affecting terpenoid biosynthesis. Inhibited rooting also resulted in a significant drop of endogenous isoprenoid CK bioactive-free bases and ribosides as well as CK N-glycoconjugates and in decreased trans-zeatin (transZ):cis-zeatin (cisZ) ratio in the aerials. Marked impairment of the structural organization of the photosynthetic apparatus and chloroplast architecture were also observed in samples with suppressed rooting. It is well known that in the plant cell monoterpenoid and transZ-type CKs biogenesis are spatially bound to plastids, while sesquiterpenoid and cisZ production are compartmented in the cytosol. In the present work, interplay between the biosynthesis of terpenoids and CK bioactive free bases and ribosides in A. alba in vitro via possible moderation of chloroplast structure has been hypothesized.     

Dynamics of Endogenous Phytohormones during Desiccation and Recovery of the Resurrection Plant Species Haberlea rhodopensis

Drought is one of the most significant threats to world agriculture and hampers the supply of food and energy. The mechanisms of drought responses can be studied using resurrection plants that are able to survive extreme dehydration. As plant hormones function in an intensive cross-talk, playing important regulatory roles in the perception and response to unfavorable environments, the dynamics of phytohormones was followed in the resurrection plant Haberlea rhodopensis Friv. during desiccation and subsequent recovery. Analysis of both leaves and roots revealed that jasmonic acid, along with and even earlier than abscisic acid, serves as a signal triggering the response of the resurrection plants to desiccation. The steady high levels of salicylic acid could be considered an integral part of the specific set of parameters that prime H. rhodopensis desiccation tolerance. The dynamic changes of cytokinins and auxins suggest that these hormones actively participate in the dehydration response and development of desiccation tolerance in the resurrection plants. Our data contribute to the elucidation of a global complex picture of the resurrection plant’s ability to withstand desiccation, which might be successfully utilized in crop improvement.     

Determination of elastomeric foam parameters for simulations of complex loading

Background: Finite element (FE) analysis has shown promise for the evaluation of elastomeric foam personal protection devices. Although appropriate representation of foam materials is necessary in order to obtain realistic simulation results, material definitions used in the literature vary widely and often fail to account for the multi-mode loading experienced by these devices. This study aims to provide a library of elastomeric foam material parameters that can be used in FE simulations of complex loading scenarios.

Method of Approach: Twelve foam materials used in footwear were tested in uni-axial compression, simple shear and volumetric compression. For each material, parameters for a common compressible hyperelastic material model used in FE analysis were determined using: (a) compression; (b) compression and shear data; and (c) data from all three tests.

Results: Material parameters and Drucker stability limits for the best fits are provided with their associated errors. The material model was able to reproduce deformation modes for which data was provided during parameter determination but was unable to predict behavior in other deformation modes.

Conclusions: Simulation results were found to be highly dependent on the extent of the test data used to determine the parameters in the material definition. This finding calls into question the many published results of simulations of complex loading that use foam material parameters obtained from a single mode of testing. The library of foam parameters developed here presents associated errors in three deformation modes that should provide for a more informed selection of material parameters.     

Patient Reported Outcomes (PROs) in Clinical Trials: Is ‘In-Trial’ Guidance Lacking? A Systematic Review

Background

Patient reported outcomes (PROs) are increasingly assessed in clinical trials, and guidelines are available to inform the design and reporting of such trials. However, researchers involved in PRO data collection report that specific guidance on ‘in-trial’ activity (recruitment, data collection and data inputting) and the management of ‘concerning’ PRO data (i.e., data which raises concern for the well-being of the trial participant) appears to be lacking. The purpose of this review was to determine the extent and nature of published guidelines addressing these areas.

Methods and Findings

Systematic review of 1,362 articles identified 18 eligible papers containing ‘in-trial’ guidelines. Two independent authors undertook a qualitative content analysis of the selected papers. Guidelines presented in each of the articles were coded according to an a priori defined coding frame, which demonstrated reliability (pooled Kappa 0.86–0.97), and validity (<2% residual category coding). The majority of guidelines present were concerned with ‘pre-trial’ activities (72%), for example, outcome measure selection and study design issues, or ‘post-trial’ activities (16%) such as data analysis, reporting and interpretation. ‘In-trial’ guidelines represented 9.2% of all guidance across the papers reviewed, with content primarily focused on compliance, quality control, proxy assessment and reporting of data collection. There were no guidelines surrounding the management of concerning PRO data.

Conclusions

The findings highlight there are minimal in-trial guidelines in publication regarding PRO data collection and management in clinical trials. No guidance appears to exist for researchers involved with the handling of concerning PRO data. Guidelines are needed, which support researchers to manage all PRO data appropriately and which facilitate unbiased data collection.     

Cytokinins in the bryophyte Physcomitrella patens: analyses of activity, distribution, and cytokinin oxidase/dehydrogenase overexpression reveal the role of extracellular cytokinins

Ultra-performance liquid chromatography-tandem mass spectrometry was used to establish the cytokinin profile of the bryophyte Physcomitrella patens (Hedw.) B.S.G.; of 40 analyzed cytokinins, 20 were detected. cis-Zeatin-riboside-O-glucoside, N(6)-(Delta(2)-isopentenyl)adenosine-5'-monophosphate (iPRMP), and trans-zeatin-riboside-O-glucoside were the most abundant intracellular cytokinins. In addition, the aromatic cytokinins N(6)-benzyladenosine (BAR), N(6)-benzyladenine, meta-, and ortho-topolin were detected. Unexpectedly, the most abundant extracellular cytokinin was the nucleotide iPRMP, and its identity was confirmed by quadrupole time-of-flight mass spectrometry. The effects of overexpressing a heterologous cytokinin oxidase/dehydrogenase (CKX; EC 1.4.3.18/1.5.99.12) gene (AtCKX2 from Arabidopsis [Arabidopsis thaliana]) on the intracellular and extracellular distribution of cytokinins was assessed. In cultures of CKX-transformed plants, ultra-performance liquid chromatography-tandem mass spectrometry measurements showed that there were pronounced reductions in the extracellular concentrations of N(6)-(Delta(2)-isopentenyl)adenine (iP) and N(6)-(Delta(2)-isopentenyl)adenosine (iPR), but their intracellular cytokinin concentrations were only slightly affected. In vitro and in vivo measured CKX activity was shown to be strongly increased in the transformants. Major phenotypic changes observed in the CKX-overexpressing plants included reduced and retarded budding, absence of sexual reproduction, and abnormal protonema cells. In bud-induction bioassays with wild-type Physcomitrella, the nucleotides iPRMP, trans-zeatin-riboside-5'-monophosphate, BAR monophosphate, and the cis-zeatin forms cZ and cZR had no detectable effects, while the activities displayed by other selected cytokinins were in the following order: iP > tZ > N(6)-benzyladenine > BAR > iPR > tZR > meta-topolin > dihydrozeatin > ortho-topolin. The results on wild type and CKX transgenics suggest that extracellular iP and iPR are the main cytokinins responsible for inducing buds in the bryophyte Physcomitrella. Cytokinin profile is discussed regarding the evolution of cytokinin biosynthetic pathways.     

Host-interactor screens of Phytophthora infestans RXLR proteins reveal vesicle trafficking as a major effector-targeted process

Pathogens modulate plant cell structure and function by secreting effectors into host tissues. Effectors typically function by associating with host molecules and modulating their activities. This study aimed to identify the host processes targeted by the RXLR class of host-translocated effectors of the potato blight pathogen Phytophthora infestans. To this end, we performed an in planta protein–protein interaction screen by transiently expressing P. infestans RXLR effectors in Nicotiana benthamiana leaves followed by coimmunoprecipitation and liquid chromatography-tandem mass spectrometry. This screen generated an effector–host protein interactome matrix of 59 P. infestans RXLR effectors x 586 N. benthamiana proteins. Classification of the host interactors into putative functional categories revealed over 35 biological processes possibly targeted by P. infestans. We further characterized the PexRD12/31 family of RXLR-WY effectors, which associate and colocalize with components of the vesicle trafficking machinery. One member of this family, PexRD31, increased the number of FYVE positive vesicles in N. benthamiana cells. FYVE positive vesicles also accumulated in leaf cells near P. infestans hyphae, indicating that the pathogen may enhance endosomal trafficking during infection. This interactome dataset will serve as a useful resource for functional studies of P. infestans effectors and of effector-targeted host processes.

One-sentence summary In planta protein–protein interaction screen of Phytophthora infestans RXLR effectors by proteomics approach reveals host vesicle trafficking as a major effector-targeted process.