A basis set for peptides for the variational approach to conformational kinetics

Although Markov state models have proven to be powerful tools in resolving the complex features of biomolecular kinetics, the discretization of the conformational space has been a bottleneck since the advent of the method. A recently introduced variational approach, which uses basis functions instead of crisp conformational states, opened up a route to construct kinetic models in which the discretization error can be controlled systematically. Here, we develop and test a basis set for peptides to be used in the variational approach. The basis set is constructed by combining local residue-centered kinetic modes that are obtained from kinetic models of terminally blocked amino acids. Using this basis set, we model the conformational kinetics of two hexapeptides with sequences VGLAPG and VGVAPG. Six basis functions are sufficient to represent the slow kinetic modes of these peptides. The basis set also allows for a direct interpretation of the slow kinetic modes without an additional clustering in the space of the dominant eigenvectors. Moreover, changes in the conformational kinetics due to the exchange of leucine in VGLAPG to valine in VGVAPG can be directly quantified by comparing histograms of the basis set expansion coefficients

Molecular dynamics simulations data of the twenty encoded amino acids in different force fields

We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5,6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalinietal.,2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8]

Natural Phenyldihydroisocoumarins: Sources, Chemistry and Bioactivity:

The present review gives an overview about naturally occurring phenyldihydroisocoumarins, their sources, and bioactivities. In total, 54 compounds are covered, including eight substances which are in fact alkaloids or protoalkaloids. These nitrogen containing compounds were exclusively found in the Papaveraceae family. The remaining 46 compounds have been reported from twelve different source families, ranging from mosses to angiosperms. Six of the nitrogen free compounds feature additional rings, while 40 are simple phenyldihydroisocoumarins with substituents in all possible positions, except 3, 2', and 6'. Common substituents of these simple phenyldihydroisocoumarins are hydroxy groups, methoxy groups, and glucosyloxy groups; on the other hand, acuminosyloxy and rutinosyloxy groups have so far been found only in one and two naturally occurring phenyldihydroisocoumarins, respectively. Though a number of bioactivities have been proven for phenyldihydroisocoumarins, ranging from anticancer and antidiabetic to antimicrobial and anti-inflammatory activities, so far only one taxon, Hydrangea macrophylla var. thunbergii, is widely used. Moreover, the usage of this taxon is mainly due to the sweet taste properties of the contained phenyldihydroisocoumarin phyllodulcin and less based on the alleged health-promoting effects of its constituents

L'uso delle reti sociali per la costruzione di campioni probabilistici: possibilità e limiti per lo studio di popolazioni senza lista di campionamento

Il campionamento a valanga è considerato un tipo di campionamento non probabilistico, la cui rappresentatività può essere valutata solo sulla base di considerazioni soggettive. D’altro canto esso risulta spesso il solo praticamente utilizzabile nel caso di popolazioni senza lista di campionamento. La tesi si divide in due parti. La prima, teorica, descrive alcuni tentativi proposti in letteratura di ricondurre le forme di campionamento a valanga nell’alveo dei campionamenti probabilistici; tra questi è degno di nota il Respondent Driven Sampling, un disegno campionario che dovrebbe combinare il campionamento a valanga con un modello matematico che pesa le unità estratte in modo da compensare la non casualità dell’estrazione e permettere così l’inferenza statistica. La seconda, empirica, indaga le prestazioni del RDS sia attraverso simulazioni sia con una web-survey su una comunità virtuale in Internet, di cui si conoscono la struttura delle relazioni e alcune caratteristiche demografiche per ogni individuo. Le stime RDS, calcolate a partire dai dati delle simulazioni e della web-survey, sono confrontate con i valori veri della popolazione e le potenziali fonti di distorsione (in particolare quelle relative all’assunzione di reclutamento casuale) sono analizzate.Populations without sampling frame are inherently hard to sample by conventional sampling designs. Often the only practical methods of obtaining the sample involve following social links from some initially identified respondents to add more research participants to the sample. These kinds of link-tracing designs make the sample liable to various forms of bias and make extremely difficult to generalize the results to the population studied. This thesis is divided into two parts. The first part of the thesis describes some attempts to build a statistical theory of link-tracing designs and illustrates, deeply, the Respondent-Driven Sampling, a link-tracing sampling design that should allow researchers to make, in populations without sampling frame, asymptotically unbiased estimates under certain conditions. The second part of the thesis investigates the performance of RDS by simulating sampling from a virtual community on the Internet, which are available in both the network structure of the population and demographic traits for each individual. In addition to simulations, this thesis tests the RDS by making a web-survey of the same population. RDS estimates from simulations and web-survey are compared to true population values and potential sources of bias (in particular those related to the random recruitment assumption) are discussed

Dynamic Properties of Force Fields

Molecular-dynamics simulations are increasingly used to study dynamic properties of biological systems. With this development, the ability of force fields to successfully predict relaxation timescales and the associated conformational exchange processes moves into focus. We assess to what extent the dynamic properties of model peptides (Ac-A-NHMe, Ac-V-NHMe, AVAVA, A10) differ when simulated with different force fields (AMBER ff99SB-ILDN, AMBER ff03, OPLS-AA/L, CHARMM27, and GROMOS43a1). The dynamic properties are extracted using Markov state models. For single-residue models (Ac-A-NHMe, Ac-V-NHMe), the slow conformational exchange processes are similar in all force fields, but the associated relaxation timescales differ by up to an order of magnitude. For the peptide systems, not only the relaxation timescales, but also the conformational exchange processes differ considerably across force fields. This finding calls the significance of dynamic interpretations of molecular-dynamics simulations into question

EFFECT OF SAR INDUCERS ON GRAPE SECONDARY METABOLITES

Fungicide application is now the most efficacious method for controlling plant diseases caused by oomycetes and fungi. As legislation is limiting and reducing their use, it is strongly stimulating studies for the identification of additional and environmentally friendly approaches in the control of their associated diseases. Among these, systemic acquired resistance (SAR) offers the prospect of long-lasting, broad-spectrum disease control through activation of the resistance defence machinery of the plant itself. Plant activators are products employed in crop protection able to elicit SAR. Therefore, they may trigger the plant own defence response against pathogen attacks, mainly stimulating mechanisms such as the biosynthesis of phytoalexins, plant secondary metabolites with a broad spectrum biological activity. In this study, two plant defence inducers, benzothiadiazole (BTH) and chitosan (CHT), deserving particular attention because of their efficacy and low toxicity, have been used. CHT is a natural and low-cost polymer (from the waste products of the crustacean carapace), obtained by chitin deacetylation. Its effectiveness is higher when molecular weight is between 10 and 100 kD and the deacetylation degree range is from 80 to 90 percent. BTH [benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester] is a synthetic compound and a functional analogue of salicylic acid, a plant hormone-like compound deeply involved in resistance against pathogens. Two different phytoiatric campaigns were planned, in 2009 and 2010, on two red grapevine (Vitis vinifera L.) varieties cultivated in experimental vineyards located at distinct sites: Groppello, an autochthonous cultivar of Lombardia, at Raffa di Puegnago (Brescia), and Merlot at Conegliano Veneto (Treviso). Open field treatments carried out on Groppello grapevines were: i) 0.03% (w/v) CHT (76 kDa molecular weight and 85% deacetylation degree), ii) 0.03% CHT in combination with 150 g hL-1 copper hydroxide (CHT/Cu) and iii) 0.3 mM BTH; whereas, on Merlot, besides CHT and CHT/Cu, BTH were replaced by 300 g hL-1 potassium phosphites. Untreated vines were used as negative control, while plants treated with conventional fungicides (penconazole and methyldinocap) were the positive control. In both field surveys, the trial was set up as a complete randomized block design in 4 replications, with 10 vines (a parcel) per treatment in each block. Plants were sprayed approximately every 10 days, according to the meteorological conditions, from the beginning of grape susceptibility to fungal diseases until the complete v\ue9raison. The phytosanitary status of vineyards was assessed weekly on leaves and bunches, by visual inspections, though both sites were not particularly predisposed to severe fungal or other epidemics. The epidemiological evaluations were performed on bunches alone and infection indexes were calculated. All the treatments were effective in controlling fungal infections (downy mildew, Plasmopara viticola and powdery mildew, Erysiphe necator), in terms of disease incidence (I %), disease severity (S %) and infection degree (ID %), though these indexes were low in untreated control grapevines, particularly in 2010. Sampling was scheduled at two phenological phases: pre-v\ue9raison and 100% v\ue9raison; bunches were randomly collected from plants during the morning and stored at -20 \ub0C until analyses. Berry tissues were separated into skin, flesh and seeds, powdered and extracted. Then, extracts were tested to evaluate their melatonin levels [by ultra performance liquid chromatography (UPLC)-MS/MS], total polyphenols (TP, by Folin-Ciocalteau assay) and antiradical activity [by DPPH, 2,2-diphenyl-1-pycryl hydrazyl and ABTS, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) assay]. Groppello and Merlot experimental wines were produced, by standard microvinification techniques, in the Centro Vitivinicolo Provinciale of Brescia and Centro di Ricerca per la Viticoltura of Conegliano (TV), respectively, and stored at 4 \ub0C in the dark until analyses. Microvinificates were produced from grapes treated with both elicitors and conventional fungicides (controls), and the following analyses, besides those also conducted for all berry tissues, were carried out: tryptophan, serotonin and melatonin detection (by UPLC-MS/MS); content of cis and trans resveratrol (by UPLC-MS/MS); levels of mycotoxins (manly ochratoxin A, OTA, by UPLC-MS/MS). In general, berry tissues treated with elicitors and the corresponding experimental wines showed higher levels of melatonin and polyphenols, as well as a higher antiradical activity than samples treated with conventional fungicides. High concentrations of tryptophan were detected in all samples, contrary to serotonin, which was not detected. The most effective elictors were CHT/Cu and CHT. In all wines, the level of OTA was below the allowable threshold of 2 ng/mL. To the best of our knowledge, these results represent the first data on the effects of agrochemicals on the melatonin content of red wine, and the presence of melatonin was reported, for the first time, in berry seeds and flash, after its previously detection in skin. Furthermore, the level of the indolamine in berry tissues varies according to the phenological stage, resulting more abundant in seed at pre-v\ue9raison and in skin at v\ue9raison. The good agreement between the data obtained in 2009 and 2010 for Groppello cultivar, and, in 2009, between Groppello and Merlot varieties cultivated in different geographical areas, suggests that, in general, plant activators may improve some qualitative/healthy treats ascribed to red wine, though their efficacy in controlling grapevine fungal diseases should be better ascertained. Finally, the role of melatonin, a powerful antioxidant, in grapevine physiology is still somewhat obscure. It is possible that, at pre-v\ue9raison, when skin anthocyanic pigmentation is still lacking, this compound may defend berry from damage due to photooxidation or UV radiation, whereas, at v\ue9raison, the indolamine may protect the germ tissues, particularly rich in storage lipids and membranes and vulnerable to oxidative damage. In conclusion, the possibility of enhancing the pharmaconutritional potential of grape/wine with phytosanitary treatments should be further tajen into account

Vapor and Liquid Phase Profiles of Essential Oils from Abies, Picea and Pinus Species and Their Phytotoxic Interactions with Weed Growth in Pre- and Post-Emergence Conditions

The chemical content of essential oils (EO) obtained from the leaves of four Pinaceae (Abies alba, Picea abies, Pinus cembra and Pinus mugo) was investigated by SPME-GC-MS technique. The vapor phase was characterized by the monoterpenes with values higher than 95.0%. Among them, a-pinene (24.7–48.5%), limonene (17.2–33.1%) and b-myrcene (9.2–27.8%) were the most abundant. The monoterpenic fraction prevailed over the sesquiterpenic one ( 74.7%) in the EO liquid phase. Limonene was the major compound in A. alba (30.4%), P. abies (20.3%) and P. mugo (78.5%), while a-pinene in P. cembra (36.2%). Regarding the phytotoxic properties, EOs were studied at different doses (2–100 L) and concentrations (2–20/100 L/mL). All EOs were found to be significantly active (p-value < 0.05) against the two recipient species in a dose-dependent way. In pre-emergence tests, germination of Lolium multiflorum and Sinapis alba was reduced by up to 62–66% and 65–82%, respectively, as well as their growth by up to 60–74% and 65–67%, due to the effects of compounds in both the vapor and liquid phases. In post-emergence cconditions, at the highest concentration, the phytotoxicity of EOs caused heavy symptoms and, in the case of S. alba, A. alba EO completely destroyed (100%) the treated seedlings

Uncovering the circadian output pathways of Neurospora crassa

The ubiquity of circadian systems has allowed their characterization in a broad range of model systems, which has greatly improved knowledge of how these systems are organized and the vast range of cellular and organismal processes under circadian control. Most of the advances, however, have come in describing the central oscillators of these systems, and, in some cases, the input pathways used to coordinate these oscillators to external time. Very little progress has been made in understanding the output pathways that allow circadian systems to regulate the breadth of processes shown to be clock-controlled. A genetic selection was designed to obtain mutations in genes involved in circadianregulated expression of the Neurospora crassa ccg-1 and ccg-2 genes. Some, but not all, of the strains obtained display altered regulation of more than one ccg as well as an ‘Easlike’ appearance on solid media, and altered circadian period on race tubes. The data suggest a model in which output from the clock to these two genes is through a single, bifurcated pathway. The cloning of the gene mutated (rrg-1) in one of the strains from the above selection led to the first molecular description of a circadian output pathway in Neurospora, the HOG MAP kinase pathway. The HOG pathway has been previously described with regard to its role in the osmotic-stress response. The discovery of the involvement of rrg-1 in circadian regulation of ccg-1 and ccg-2 led to the discovery of regulation of the HOG pathway by the circadian clock. The data indicate that osmotic stress information and time-of-day information are transduced through the HOG pathway and implicate a role for the clock in preparing the organism for daily occurrences of hyperosmotic stress associated with sun exposure. The genetic selection, and the description of the HOG pathway with regard to circadian output, provide a basis for further characterization of circadian output in Neurospora. The ubiquity of MAP kinase pathways, such as the HOG pathway, and the observed similarities in the mechanisms of circadian clock function across multiple phyla, indicate that these findings may well be applicable to other model systems

Impact of Cooking on Bioactive Compounds and Antioxidant Activity of Pigmented Rice Cultivars

Pigmented rice cultivars, namely Venere and Artemide, are a source of bioactive molecules, in particular phenolics, including anthocyanins, exerting a positive effect on cardiovascular systems thanks also to their antioxidant capacity. This study aimed to determine the total phenol index (TPI), total flavonoids (TF), total anthocyanins (TA) and in vitro antioxidant capacity in 12 batches of Venere cultivar and two batches of Artemide cultivar. The rice was cooked using different methods (boiling, microwave, pressure cooker, water bath, rice cooker) with the purpose to individuate the procedure limiting the loss of bioactive compounds. TPI, TF and TA were spectrophotometrically determined in both raw and cooked rice samples. Rice samples of Artemide cultivars were richer in TPI (17.7-18.8 vs. 8.2-11.9 g gallic acid/kg in Venere rice), TF (13.1 vs. 5.0-7.1 g catechin/kg rice for Venere rice) and TA (3.2-3.4 vs. 1.8-2.9 g Cy-3glc/kg for Venere rice) in comparison to those of Venere cultivar; as well, they showed higher antioxidant capacity (46.6-47.8 vs. 14.4-31.9 mM Trolox/kg for Venere rice). Among the investigated cooking methods, the rice cooker and the water bath led to lower and comparable losses of phenolics. Interestingly, the cooking water remaining after cooking with the rice cooker was rich in phenolics. The consumption of a portion of rice (100 g) cooked with the rice cooker with its own cooking water can supply 240 mg catechin and 711 mg cyanidin 3-O-glucoside for Venere rice and 545 mg catechin and 614 mg cyanidin 3-O-glucoside for Artemide rice, with a potential positive effect on health

Validation of a method for diosgenin extraction from fenugreek (Trigonella foenum-graecum L.)

Background. Diosgenin is a very important plant secondary metabolite and raw material for the drug industry. Plant sources rich in diosgenin include yam (Dioscorea spp.) and fenugreek (Trigonella foenum-graecum L.). A method for diosgenin extraction from yam extracts has previously been validated, but its extraction from fenugreek plants still requires validation. In addition, all available methods require time-consuming additional purification steps. The present study was aimed at developing a low cost, less time-consuming single-step method for diosgenin extraction from fenugreek. Material and methods. This study represents a method developed for diosgenin extraction from fenugreek plants without any additional/supportive purification methods such as chromatography or thin-layer chromatography. Diosgenin yield estimation and purity analysis by HPLC method, along with accuracy and precision analysis, is presented. Results. Five different fenugreek varieties were subjected to a newly developed diosgenin extraction method, and an HPLC chromatogram showed a single peak corresponding to diosgenin. Yield was determined by the standard curve method. Limit of detection (LOD) and limit of quantification (LOQ) for the assay were found to be 0.0312 and 0.102 \u3bcg, respectively; t calculated for slope and other statistical parameters were found to be significant (P value < 0.001) for this method. Conclusion. We have developed a fast, accurate and low cost method for diosgenin extraction from fenugreek. Although the authors have studied this method only in fenugreek plants, it could be applied to the extraction of a few other plant secondary metabolites, which will help researchers to save time and effort