The Effects of Melatonin on Transcriptional Profile of Unfolded Protein Response Genes Under Endoplasmic Reticulum Stress in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

When the load of secretory pathway is increased or folding capacity in the endoplasmic reticulum (ER) is insufficient, unfolded proteins might accumulate in ER lumen causing a phenomenon called ER stress. During ER stress, normal cell functions are suppressed and unfolded protein response (UPR) is induced. Studies in animal systems suggest that melatonin alleviates the detrimental effects of ER stress; however, there is no study in plants in this respect. Hence, in this study, we investigated the possible role of melatonin on alleviation of ER stress in model plant Arabidopsis thaliana. Tunicamycin (Tm) was used to specifically induce ER stress. Melatonin treatment (10 and 25 μM but not 1 μM) increased root growth under Tm treatment, but it did not reach control levels. ER stress induced the expressions of ER stress sensor/transducer genes, ER chaperones and folding helper genes, ER-associated degradation (ERAD) genes, and ER stress-associated apoptosis genes in roots and shoots (a total of 16 genes). Among them, the expressions of ER stress sensor/transducer bZIP17, bZIP28, IRE1A, IRE1B, ERAD-related SEL1, and apoptosis genes AGB1 were decreased back to control levels with 25 μM melatonin under ER stress in roots. Moreover, Tm?+?melatonin treatments decreased the expressions of these genes when compared to only Tm-treated plants. Downregulation of UPR components with increased concentrations of melatonin under Tm treatment demonstrated that melatonin alleviated the detrimental effects of ER stress.     

The effects of biological rhythms and sleep quality on benign paroxysmal positional vertigo and reflux symptom severity

Recently, there has been increased interest in chronotypes and clinical differences between them. However, there is limited information about the potential influence of the chronotypes on clinical manifestations and symptom intensity of somatic diseases. The aim of this study is to evaluate the impact of biological rhythm differences and sleep quality on benign paroxysmal positional vertigo (BPPV) and larengo pharyngeal reflux (LPR) severity. Forty-four LPR patients, 43 BBPV patients and 42 controls were included in the study. The morningness–eveningness questionnaire was used to determine chronotypes, and the Pittsburgh Sleep Quality Index was used to assess subjective sleep quality. Both patient groups reported a significantly greater tendency to eveningness diurnal preferences compared to healthy controls. As with the circadian preferences, patients with BPPV or LPR characterized by poorer sleep quality and worse insomnia than non-patient individuals. It can be concluded that the circadian rhythm and sleep quality are related to the severity of LPR and BPPV.     

Determination of endogenous hormones, sugars and mineral nutrition levels during the induction, initiation and differentiation stage and their effects on flower formation in olive

Olive (Olea europaea L.) is one of the most important crop plants grown in the Mediterranean region. Varying levels of hormones, sugars and mineral nutrient are thought to influence flower bud formation. The objective of this study was to evaluate the changes in endogenous sugar, mineral nutrition and hormone levels in leaf, node and fruit samples of Memecik olive during the induction, initiation and differentiation periods in on (bearing) and off (non-bearing) years. Leaf, node and fruit samples of mature 15-year-old Memecik olive were used. The samples were taken during the induction, initiation and differentiation periods of olive in on (2000) and off (2001) years. Sugar (glucose, fructose and sucrose), mineral nutrient (N, P, K, Ca, Mg, Fe, Zn, Mn and Cu) and hormone [abscisic acid (ABA), indole acetic acid (IAA), gibberellic acid (GA₃, GA₄) and zeatin (Z)] levels were determined in on and off years. Hormone and sugar levels were measured by gas chromatography and high-performance liquid chromatography. The K, Ca, Mg, Fe, Mn, Zn and Cu levels were quantified by an atomic absorption spectrophotometry. Nitrogen was determined by the Kjeldahl procedure, and P by a spectrophotometric method. The differences in any of the sugar concentrations, with the exception of fructose, were not significant in on and off years. Hormone levels, however, were significantly different in on and off years. Glucose had the highest concentrations in both years, followed by sucrose and fructose, respectively. The highest macro and micro element concentrations were found to be Ca and Fe, respectively. Thus, the results suggest that carbohydrates and mineral nutrients may not have a direct effect to induce flower initiation. However, high GA₃ level exhibited an inhibitory effect on floral formation during the induction and initiation periods. On the other hand, the high concentrations of GA₄, ABA and certain cytokinin levels may have a positive effect on flower formation in olive during the induction and initiation periods.     

Fitting of dynamic recurrent neural network models to sensory stimulus-response data

We present a theoretical study aiming at model fitting for sensory neurons. Conventional neural network training approaches are not applicable to this problem due to lack of continuous data. Although the stimulus can be considered as a smooth time-dependent variable, the associated response will be a set of neural spike timings (roughly the instants of successive action potential peaks) that have no amplitude information. A recurrent neural network model can be fitted to such a stimulus-response data pair by using the maximum likelihood estimation method where the likelihood function is derived from Poisson statistics of neural spiking. The universal approximation feature of the recurrent dynamical neuron network models allows us to describe excitatory-inhibitory characteristics of an actual sensory neural network with any desired number of neurons. The stimulus data are generated by a phased cosine Fourier series having a fixed amplitude and frequency but a randomly shot phase. Various values of amplitude, stimulus component size, and sample size are applied in order to examine the effect of the stimulus to the identification process. Results are presented in tabular and graphical forms at the end of this text. In addition, to demonstrate the success of this research, a study involving the same model, nominal parameters and stimulus structure, and another study that works on different models are compared to that of this research.     

Robustness from flexibility in the fungal circadian clock

Background  

Robustness is a central property of living systems, enabling function to be maintained against environmental perturbations. A key challenge is to identify the structures in biological circuits that confer system-level properties such as robustness. Circadian clocks allow organisms to adapt to the predictable changes of the 24-hour day/night cycle by generating endogenous rhythms that can be entrained to the external cycle. In all organisms, the clock circuits typically comprise multiple interlocked feedback loops controlling the rhythmic expression of key genes. Previously, we showed that such architectures increase the flexibility of the clock's rhythmic behaviour. We now test the relationship between flexibility and robustness, using a mathematical model of the circuit controlling conidiation in the fungus Neurospora crassa.     

RNA-Mediated Feedback Control of Transcriptional Condensates

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Crystal structures of NodS N-methyltransferase from Bradyrhizobium japonicum in ligand-free form and as SAH complex

NodS is an S-adenosyl-l-methionine (SAM)-dependent N-methyltransferase that is involved in the biosynthesis of Nod factor (NF) in rhizobia, which are bacterial symbionts of legume plants. NF is a modified chitooligosaccharide (COS) signal molecule that is recognized by the legume host, where it initiates symbiotic processes leading to atmospheric nitrogen fixation. We report the crystal structure of recombinant NodS protein from Bradyrhizobium japonicum, which infects lupine and serradella legumes. Two crystal forms—ligand-free NodS and NodS in complex with S-adenosyl-l-homocysteine, which is a by-product of the methylation reaction—were obtained, and their structures were refined to resolutions of 2.43 Å and 1.85 Å, respectively. Although the overall fold (consisting of a seven-stranded β-sheet flanked by layers of helices) is similar to those of other SAM-dependent methyltransferases, NodS has specific features reflecting the unique character of its oligosaccharide substrate. In particular, the N-terminal helix and its connecting loop get ordered upon SAM binding, thereby closing the methyl donor cavity and shaping a long surface canyon that is clearly the binding site for the acceptor molecule. Comparison of the two structural forms of NodS suggests that there are also other conformational changes taking place upon the binding of the donor substrate. As an enzyme that methylates a COS substrate, NodS is the first example among all SAM-dependent methyltransferases to have its three-dimensional structure elucidated. Gaining insight about how NodS binds its donor and acceptor substrates helps to better understand the mechanism of NodS activity and the basis of its functional difference in various rhizobia.