Beyond the photocycle-how cryptochromes regulate photoresponses in plants?

Cryptochromes (CRYs) are blue light receptors that mediate light regulation of plant growth and development. Land plants possess various numbers of cryptochromes, CRY1 and CRY2, which serve overlapping and partially redundant functions in different plant species. Cryptochromes exist as physiologically inactive monomers in darkness; photoexcited cryptochromes undergo homodimerization to increase their affinity to the CRY-signaling proteins, such as CIBs (CRY2-interacting bHLH), PIFs (Phytochrome-Interacting Factors), AUX/IAA (Auxin/INDOLE-3-ACETIC ACID), and the COP1-SPAs (Constitutive Photomorphogenesis 1-Suppressors of Phytochrome A) complexes. These light-dependent protein-protein interactions alter the activity of the CRY-signaling proteins to change gene expression and developmental programs in response to light. In the meantime, photoexcitation also changes the affinity of cryptochromes to the CRY-regulatory proteins, such as BICs (Blue-light Inhibitors of CRYs) and PPKs (Photoregulatory Protein Kinases), to modulate the activity, modification, or abundance of cryptochromes and photosensitivity of plants in response to the changing light environment

A CRY-BIC negative-feedback circuitry regulating blue light sensitivity of Arabidopsis.

Cryptochromes are blue light receptors that regulate various light responses in plants. Arabidopsis cryptochrome 1 (CRY1) and cryptochrome 2 (CRY2) mediate blue light inhibition of hypocotyl elongation and long-day (LD) promotion of floral initiation. It has been reported recently that two negative regulators of Arabidopsis cryptochromes, Blue light Inhibitors of Cryptochromes 1 and 2 (BIC1 and BIC2), inhibit cryptochrome function by blocking blue light-dependent cryptochrome dimerization. However, it remained unclear how cryptochromes regulate the BIC gene activity. Here we show that cryptochromes mediate light activation of transcription of the BIC genes, by suppressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), resulting in activation of the transcription activator ELONGATED HYPOCOTYL 5 (HY5) that is associated with chromatins of the BIC promoters. These results demonstrate a CRY-BIC negative-feedback circuitry that regulates the activity of each other. Surprisingly, phytochromes also mediate light activation of BIC transcription, suggesting a novel photoreceptor co-action mechanism to sustain blue light sensitivity of plants under the broad spectra of solar radiation in nature

Immunohistochemical localization of galectin-3 in the granulomatous lesions of paratuberculosis-infected bovine intestine

The presence of galectin-3 was immunohistochemically quantified in bovine intestines infected with paratuberculosis (Johne's disease) to determine whether galectin-3 was involved in the formation of granulation tissue associated with the disease. Mycobacterium avium subsp. paratuberculosis infection was histochemically confirmed using Ziehl-Neelsen staining and molecularly diagnosed through rpoB DNA sequencing. Galectin-3 was detected in the majority of inflammatory cells, possibly macrophages, in the granulomatous lesions within affected tissues, including the ileum. These findings suggest that galectin-3 is associated with the formation of chronic granulation tissues in bovine paratuberculosis, probably through cell adhesion and anti-apoptosis mechanisms

Adiabatic perturbation theory and geometry of periodically-driven systems

We give a systematic review of the adiabatic theorem and the leading non-adiabatic corrections in periodically-driven (Floquet) systems. These corrections have a two-fold origin: (i) conventional ones originating from the gradually changing Floquet Hamiltonian and (ii) corrections originating from changing the micro-motion operator. These corrections conspire to give a Hall-type linear response for non-stroboscopic (time-averaged) observables allowing one to measure the Berry curvature and the Chern number related to the Floquet Hamiltonian, thus extending these concepts to periodically-driven many-body systems. The non-zero Floquet Chern number allows one to realize a Thouless energy pump, where one can adiabatically add energy to the system in discrete units of the driving frequency. We discuss the validity of Floquet Adiabatic Perturbation Theory (FAPT) using five different models covering linear and non-linear few and many-particle systems. We argue that in interacting systems, even in the stable high-frequency regimes, FAPT breaks down at ultra slow ramp rates due to avoided crossings of photon resonances, not captured by the inverse-frequency expansion, leading to a counter-intuitive stronger heating at slower ramp rates. Nevertheless, large windows in the ramp rate are shown to exist for which the physics of interacting driven systems is well captured by FAPT.The authors would like to thank M. Aidelsburger, M. Atala, E. Dalla Torre, N. Goldman, M. Heyl, D. Huse, G. Jotzu, C. Kennedy, M. Lohse, T. Mori, L. Pollet, M. Rudner, A. Russomanno, and C. Schweizer for fruitful discussions. This work was supported by AFOSR FA9550-16-1-0334, NSF DMR-1506340, ARO W911NF1410540, and the Hungarian research grant OTKA Nos. K101244, K105149. M. K. was supported by Laboratory Directed Research and Development (LDRD) funding from Berkeley Lab, provided by the Director, Office of Science, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The authors are pleased to acknowledge that the computational work reported in this paper was performed on the Shared Computing Cluster which is administered by Boston University's Research Computing Services. The authors also acknowledge the Research Computing Services group for providing consulting support which has contributed to the results reported within this paper. The study of the driven non-integrable transverse-field Ising model was carried out using QuSpin [185] - an open-source state-of-the-art Python package for dynamics and exact diagonalization of quantum many body systems, available to download here. (FA9550-16-1-0334 - AFOSR; DMR-1506340 - NSF; W911NF1410540 - ARO; K101244 - Hungarian research grant OTKA; K105149 - Hungarian research grant OTKA; DE-AC02-05CH11231 - Laboratory Directed Research and Development (LDRD) funding from Berkeley Lab)https://arxiv.org/pdf/1606.02229.pd

Counter-current chromatography for the separation of terpenoids: A comprehensive review with respect to the solvent systems employed

Copyright @ 2014 The Authors.This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.Natural products extracts are commonly highly complex mixtures of active compounds and consequently their purification becomes a particularly challenging task. The development of a purification protocol to extract a single active component from the many hundreds that are often present in the mixture is something that can take months or even years to achieve, thus it is important for the natural product chemist to have, at their disposal, a broad range of diverse purification techniques. Counter-current chromatography (CCC) is one such separation technique utilising two immiscible phases, one as the stationary phase (retained in a spinning coil by centrifugal forces) and the second as the mobile phase. The method benefits from a number of advantages when compared with the more traditional liquid-solid separation methods, such as no irreversible adsorption, total recovery of the injected sample, minimal tailing of peaks, low risk of sample denaturation, the ability to accept particulates, and a low solvent consumption. The selection of an appropriate two-phase solvent system is critical to the running of CCC since this is both the mobile and the stationary phase of the system. However, this is also by far the most time consuming aspect of the technique and the one that most inhibits its general take-up. In recent years, numerous natural product purifications have been published using CCC from almost every country across the globe. Many of these papers are devoted to terpenoids-one of the most diverse groups. Naturally occurring terpenoids provide opportunities to discover new drugs but many of them are available at very low levels in nature and a huge number of them still remain unexplored. The collective knowledge on performing successful CCC separations of terpenoids has been gathered and reviewed by the authors, in order to create a comprehensive document that will be of great assistance in performing future purifications. © 2014 The Author(s)

Age dependent plasticity in endocannabinoid modulation of pain processing through postnatal development

Significant age and experience-dependent remodelling of spinal and supraspinal neural networks occur resulting in altered pain responses in early life. In adults endogenous opioid peptide and endocannabinoid (ECs) pain control systems exist which modify pain responses but the role they play in acute responses to pain and postnatal neurodevelopment is unknown. Here we have studied the changing role of the ECs in brainstem nuclei essential for the control of nociception from birth to adulthood in both rat and human. Using in vivo electrophysiology we show that substantial functional changes occur in the effect of microinjection of ECs receptor agonists and antagonists in the periaqueductal grey (PAG) and rostroventral medulla (RVM), both of which play central roles in the supraspinal control of pain and the maintenance of chronic pain states in adulthood. We show that in immature PAG and RVM the orphan receptor GPR55 is able to mediate profound analgesia which is absent in adults. We show that tissue levels of endocannabinoid neurotransmitters, anandamide and 2-arachidonoylglycerol within the PAG and RVM are developmentally regulated (using mass spectrometry). The expression patterns and levels of ECs enzymes and receptors were assessed using quantitative PCR and immunohistochemistry. In human brainstem we show age-related alterations in the expression of key enzymes and receptors in involved in ECs function using PCR and in situ hybridisation. These data reveal significant changes on ECs that to this point have been unknown and which shed new light into the complex neurochemical changes that permit normal, mature responses to pain

Evolution of Plant Nucleotide-Sugar Interconversion Enzymes

Nucleotide-diphospho-sugars (NDP-sugars) are the building blocks of diverse polysaccharides and glycoconjugates in all organisms. In plants, 11 families of NDP-sugar interconversion enzymes (NSEs) have been identified, each of which interconverts one NDP-sugar to another. While the functions of these enzyme families have been characterized in various plants, very little is known about their evolution and origin. Our phylogenetic analyses indicate that all the 11 plant NSE families are distantly related and most of them originated from different progenitor genes, which have already diverged in ancient prokaryotes. For instance, all NSE families are found in the lower land plant mosses and most of them are also found in aquatic algae, implicating that they have already evolved to be capable of synthesizing all the 11 different NDP-sugars. Particularly interesting is that the evolution of RHM (UDP-L-rhamnose synthase) manifests the fusion of genes of three enzymatic activities in early eukaryotes in a rather intriguing manner. The plant NRS/ER (nucleotide-rhamnose synthase/epimerase-reductase), on the other hand, evolved much later from the ancient plant RHMs through losing the N-terminal domain. Based on these findings, an evolutionary model is proposed to explain the origin and evolution of different NSE families. For instance, the UGlcAE (UDP-D-glucuronic acid 4-epimerase) family is suggested to have evolved from some chlamydial bacteria. Our data also show considerably higher sequence diversity among NSE-like genes in modern prokaryotes, consistent with the higher sugar diversity found in prokaryotes. All the NSE families are widely found in plants and algae containing carbohydrate-rich cell walls, while sporadically found in animals, fungi and other eukaryotes, which do not have or have cell walls with distinct compositions. Results of this study were shown to be highly useful for identifying unknown genes for further experimental characterization to determine their functions in the synthesis of diverse glycosylated molecules

A single amino acid substitution confers enhanced methylation activity of mammalian Dnmt3b on chromatin DNA

Dnmt3a and Dnmt3b are paralogous enzymes responsible for de novo DNA methylation but with distinguished biological functions. In mice, disruption of Dnmt3b but not Dnmt3a causes global DNA hypomethylation, especially in repetitive sequences, which comprise the large majority of methylated DNA in the genome. By measuring DNA methylation activity of Dnmt3a and Dnmt3b homologues from five species, we found that mammalian Dnmt3b possessed significantly higher methylation activity on chromatin DNA than Dnmt3a and non-mammalian Dnmt3b. Sequence comparison and mutagenesis experiments identified a single amino acid substitution (I662N) in mammalian Dnmt3b as being crucial for its high chromatin DNA methylation activity. Further mechanistic studies demonstrated this substitution markedly enhanced the binding of Dnmt3b to nucleosomes and hence increased the chromatin DNA methylation activity. Moreover, this substitution was crucial for Dnmt3b to efficiently methylate repetitive sequences, which increased dramatically in mammalian genomes. Consistent with our observation that Dnmt3b evolved more rapidly than Dnmt3a during the emergence of mammals, these results demonstrated that the I662N substitution in mammalian Dnmt3b conferred enhanced chromatin DNA methylation activity and contributed to functional adaptation in the epigenetic system

Cross Section and Transverse Single-Spin Asymmetry of η\eta Mesons in p↑+pp^{\uparrow}+p Collisions at s=200\sqrt{s}=200 GeV at Forward Rapidity

We present a measurement of the cross section and transverse single-spin asymmetry ($A_N$) for $\eta$ mesons at large pseudorapidity from $\sqrt{s}=200$~GeV $p^{\uparrow}+p$ collisions. The measured cross section for $0.5<p_T<5.0$~GeV/$c$ and $3.0<|\eta|<3.8$ is well described by a next-to-leading-order perturbative-quantum-chromodynamics calculation. The asymmetries $A_N$ have been measured as a function of Feynman-$x$ ($x_F$) from $0.2<|x_{F}|<0.7$, as well as transverse momentum ($p_T$) from $1.0<p_T<4.5$~GeV/$c$. The asymmetry averaged over positive $x_F$ is $\langle{A_{N}}\rangle=0.061{\pm}0.014$. The results are consistent with prior transverse single-spin measurements of forward $\eta$ and $\pi^{0}$ mesons at various energies in overlapping $x_F$ ranges. Comparison of different particle species can help to determine the origin of the large observed asymmetries in $p^{\uparrow}+p$ collisions.Comment: 484 authors, 13 pages, 11 figures, 4 tables, 2008 data. v2 is version accepted by Phys. Rev. D. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be)publicly available at http://www.phenix.bnl.gov/papers.htm