All living systems acquire information about their environment. At the cellular level, they do so through signaling pathways. Such pathways rely on reversible binding interactions between molecules ...that detect and transmit the presence of an extracellular cue or signal to the cell's interior. These interactions are inherently stochastic and thus noisy. On the one hand, noise can cause a signaling pathway to produce the same response for different stimuli, which reduces the amount of information a pathway acquires. On the other hand, in processes such as stochastic resonance, noise can improve the detection of weak stimuli and thus the acquisition of information. It is not clear whether the kinetic parameters that determine a pathway's operation cause noise to reduce or increase the acquisition of information. We analyze how the kinetic properties of the reversible binding interactions used by signaling pathways affect the relationship between noise, the response to a signal, and information acquisition. Our results show that, under a wide range of biologically sensible parameter values, a noisy dynamic of reversible binding interactions is necessary to produce distinct responses to different stimuli. As a consequence, noise is indispensable for the acquisition of information in signaling pathways. Our observations go beyond previous work by showing that noise plays a positive role in signaling pathways, demonstrating that noise is essential when such pathways acquire information.
Using the constraints imposed by the crystalline symmetry of FeSe and the experimentally observed phenomenology, we analyze the possible pairing symmetry of the superconducting order parameter ...focusing on intercalated and monolayer FeSe compounds. Such analysis leads to three possible pairing symmetry states-s wave, d wave, and helical p wave. Despite the differences in the pairing symmetry, each of these states is fully gapped with gap minimum centered above the normal state Fermi surface, in agreement with photoemission data of Zhang et al. Phys. Rev. Lett. 117, 117001 (2016). The analysis provides additional insights into the possible pairing mechanism for each of these states, highlighting the detrimental role of the renormalized repulsive intraorbital Hubbard U and interorbital U′ and the beneficial role of the pair hopping J′ and the Hund's J terms, as well as the spin-orbit coupling in the effective low-energy Hamiltonian.
Abstract JAK proteins have been linked with survival and proliferation of multiple myeloma (MM) cells; therefore, JAK inhibition could be a therapeutic strategy for MM. We evaluated JAK1 and JAK2 ...expression in MM patients and the effects of JAK/STAT pathway inhibition on apoptosis, cell cycle, gene and protein expression in RPMI-8226 and U266 MM cell lines. 57% of patients presented overexpression of JAK2 and 27%, of JAK1 . After treatment with ruxolitinib and bortezomib, RPMI-8226 and U266 presented 50% of cells in late apoptosis, reduction of anti-apoptotic genes expression and higher number of cells in SubG0 phase. Co-culture with stromal cells protected RPMI-8226 cells from apoptosis, which was reversed by lenalidomide addition. Combination of ruxolitinib, bortezomib and lenalidomide induced 72% of cell death, equivalent to bortezomib, lenalidomide and dexamethasone, combination used in clinical practice. Many JAK/STAT pathway genes, after treatment, had their expression reduced, mainly in RPMI-8226, with insignificant changes in U266, and. In this scenario, JAK/STAT pathway could pose as a new therapeutic target to be exploited, since it is constitutively active and contributes to survival of MM tumor cells.
It takes two: Both a lysine and a glutamate residue in the active site of tryptophan halogenase are essential for its chlorination activity. A mechanism for the regioselective enzymatic chlorination ...of tryptophan involving both amino acids is suggested (see scheme).
During the last years halogenated compounds have drawn a lot of attention. Metabolites with one or more halogen atoms are often more active than their non-halogenated derivatives like indole-3-acetic ...acid (IAA) and 4-Cl-IAA. Within this work, bacterial flavin-dependent tryptophan halogenase genes were inserted into Brassica rapa ssp. pekinensis (Chinese cabbage) with the aim to produce novel halogenated indole compounds. It was investigated which tryptophan-derived indole metabolites, such as indole glucosinolates or potential degradation products can be synthesized by the transgenic root cultures. In vivo and in vitro activity of halogenases heterologously produced was shown and the production of chlorinated tryptophan in transgenic root lines was confirmed. Furthermore, chlorinated indole-3-acetonitrile (Cl-IAN) was detected. Other tryptophan-derived indole metabolites, such as IAA or indole glucosinolates were not found in the transgenic roots in a chlorinated form. The influence of altered growth conditions on the amount of produced chlorinated compounds was evaluated. We found an increase in Cl-IAN production at low temperatures (8 °C), but otherwise no significant changes were observed. Furthermore, we were able to regenerate the wild type and transgenic root cultures to adult plants, of which the latter still produced chlorinated metabolites. Therefore, we conclude that the genetic information had been stably integrated. The transgenic plants showed a slightly altered phenotype compared to plants grown from seeds since they also still expressed the rol genes. By this approach we were able to generate various stably transformed plant materials from which it was possible to isolate chlorinated tryptophan and Cl-IAN.
Brassica rapa has been transformed into transgenic root cultures harboring three different tryptophan-dependent halogenases from bacterial origin. These were regenerated to plants that stably contained the halogenase genes. Tryptophan was converted to Cl-tryptophan in planta and to other chlorinated indole derivatives by the plant enzymes. Display omitted
•Hairy roots of Chinese cabbage were stably transformed with bacterial halogenase genes.•Halogenated tryptophan and compounds derived from the amino acid were found.•Production of halogenated compounds was induced by cold treatment.•Transgenic root cultures were regenerated to adult plants that stably contained the halogenase genes.•Regenerated plants produced the same set of halogenated metabolites as their progenitor.
The biosynthetic gene cluster for the plant growth-regulating compound thienodolin was identified in and cloned from the producer organism Streptomyces albogriseolus MJ286-76F7. Sequence analysis of ...a 27 kb DNA region revealed the presence of 21 ORFs, 14 of which are involved in thienodolin biosynthesis. Three insertional inactivation mutants were generated in the sequenced region to analyze their involvement in thienodolin biosynthesis and to functionally characterize specific genes. The gene inactivation experiments together with enzyme assays with enzymes obtained by heterologous expression and feeding studies showed that the first step in thienodolin biosynthesis is catalyzed by a tryptophan 6-halogenase and that the last step is the formation of a carboxylic amide group catalyzed by an amidotransferase. The results led to a hypothetical model for thienodolin biosynthesis.
The understanding of biological halogenation has increased during the last few years. While haloperoxidases were the only halogenating enzymes known until 1997, it is now clear that haloperoxidases ...are hardly, if at all, involved in biosynthesis of more complex halogenated compounds in microorganisms. A novel type of halogenating enzymes, flavin-dependent halogenases, has been identified as a major player in the introduction of chloride and bromide into activated organic molecules. Flavin-dependent halogenases require the activity of a flavin reductase for the production of reduced flavin, required by the actual halogenase. A number of flavin-dependent tryptophan halogenases have been investigated in some detail, and the first three-dimensional structure of a member of this enzyme subfamily, tryptophan 7-halogenase, has been elucidated. This structure suggests a mechanism involving the formation of hypohalous acid, which is used inside the enzyme for regioselective halogenation of the respective substrate. The introduction of halogen atoms into non-activated alkyl groups is catalysed by non-heme FeII alpha-ketoglutarate- and O2-dependent halogenases. Examples for the use of flavin-dependent halogenases for the formation of novel halogenated compounds in in vitro and in vivo reactions promise a bright future for the application of biological halogenation reactions.
Benford's Law for Mixtures Balanzario, Eugenio P.
Communications in statistics. Theory and methods,
02/2015, Letnik:
44, Številka:
4
Journal Article
Recenzirano
Given a random variable ξ we present three different constructions of a family
of random variables such that
and such that a mixture of the elements of
, either satisfies Benford's law exactly, or it ...satisfies Benford's law with any preassigned degree of accuracy.
Creating more space in the active site of the tryptophan 7‐halogenase PrnA by exchanging the large amino acid phenylalanine for the smaller alanine makes it possible for the substrate to bind in ...different orientations (see picture; yellow PrnA, blue PrnAF103A variant). This results in halogenation of the differently bound substrate in the 5‐position of the indole ring.
In Streptomyces albogriseolus the indolethiophen alkaloid thienodolin is derived from tryptophan. The first step in thienodolin biosynthesis is the regioselective chlorination of tryptophan in the ...6-position of the indole ring. The second step is catalyzed by the aminotransferase ThdN. ThdN shows sequence homology (up to 69 % similarity) with known pyridoxal 5'-phosphate-dependent aminotransferases of the aspartate aminotransferase family from Gram-positive bacteria. thdN was heterologously expressed in Pseudomonas fluorescens, and the enzyme was purified by nickel-affinity chromatography. ThdN is a homodimeric enzyme with a mass of 90 600 kDa and catalyzes the conversion of l-tryptophan and a number of chlorinated and brominated l-tryptophans. The lowest K
values were found for 6-bromo- and 6-chlorotryptophan (40 and 66 μm, respectively). For l-tryptophan it was 454 μm, which explains why thienodolin is the major product and dechlorothienodolin is only a minor component. The turnover number (k
) for 7-chlorotryptophan (128 min
) was higher than that for the natural substrate 6-chlorotryptophan (88 min
).
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