Transcription-mediated supercoiling regulates genome folding and loop formation.

The chromatin fiber folds into loops, but the mechanisms controlling loop extrusion are still poorly understood. Using super-resolution microscopy, we visualize that loops in intact nuclei are formed by a scaffold of cohesin complexes from which the DNA protrudes. RNA polymerase II decorates the top of the loops and is physically segregated from cohesin. Augmented looping upon increased loading of cohesin on chromosomes causes disruption of Lamin at the nuclear rim and chromatin blending, a homogeneous distribution of chromatin within the nucleus. Altering supercoiling via either transcription or topoisomerase inhibition counteracts chromatin blending, increases chromatin condensation, disrupts loop formation, and leads to altered cohesin distribution and mobility on chromatin. Overall, negative supercoiling generated by transcription is an important regulator of loop formation in vivo.

Non-resonant inelastic X-ray scattering for discrimination of pigments.

Inelastic X-ray scattering (IXS) spectroscopy has been used in many fields of solid-state physics and theoretical chemistry as an accurate and quantitative probe of elementary excitations. We show that non-resonant IXS spectra in the energy loss range below 100 eV exhibit a strong contrast across a wide range of commercially available pigments, opening new routes for their discrimination. These signatures combine plasmonic transitions, collective excitations and low energy absorption edges. We have performed IXS to discriminate different artists' pigments within complex mixtures and to quantitatively determine rutile and anatase polymorphs of TiO2. The integration of experimental data on pigment powders with suitable ab initio simulations shows a precise fit of the spectroscopic data both in the position of the resonances and in their relative intensity.

All-electron many-body approach to resonant inelastic X-ray scattering.

We present a formalism for the resonant inelastic X-ray scattering (RIXS) cross section. The resulting compact expression in terms of polarizability matrix elements, particularly lends itself to the implementation in an all-electron many-body perturbation theory (MBPT) framework, which is realized in the full-potential package exciting. With the carbon K edge RIXS of diamond and the oxygen K edge RIXS of ß-Ga2O3, respectively, we demonstrate the importance of electron-hole correlation and atomic coherence in the RIXS spectra.

Design of auxiliary systems for spectroscopy.

The Kohn-Sham system is the prototypical example of an auxiliary system that targets, in principle exactly, an observable like the electronic density without the need to calculate the complicated many-body wavefunction. Although the Kohn-Sham system does not describe excited-state properties directly, it also represents a very successful strategy guideline for many spectroscopy applications. Here we propose a generalization of the Kohn-Sham idea. In many situations one is interested only in limited answers to specific questions, whereas in state-of-the-art approaches a lot of information is generally calculated that is not needed for the interpretation of experimental spectra. For example, when the target is a spectrum S(ω) like the optical absorption of a solid, within time-dependent density-functional theory (TDDFT) one calculates the whole response function χ(r,r',ω). Analogously, within many-body perturbation theory (MBPT) one calculates the whole one-particle Green's function G(r,r',ω), while only the total spectral function A(ω) is needed for angle-integrated photoemission spectra. In this contribution, we advocate the possibility of designing auxiliary systems with effective potentials or kernels that target only the specific spectral properties of interest and are simpler than the self-energy of MBPT or the exchange-correlation kernel of TDDFT. In particular, we discuss the fundamentals and prototypical applications of simplified effective kernels for optical absorption and spectral potentials for photoemission, and we discuss how to express these potentials or kernels as functionals of the density.

Exciton Band Structure in Two-Dimensional Materials.

Low-dimensional materials differ from their bulk counterparts in many respects. In particular, the screening of the Coulomb interaction is strongly reduced, which can have important consequences such as the significant increase of exciton binding energies. In bulk materials the binding energy is used as an indicator in optical spectra to distinguish different kinds of excitons, but this is not possible in low-dimensional materials, where the binding energy is large and comparable in size for excitons of very different localization. Here we demonstrate that the exciton band structure, which can be accessed experimentally, instead provides a powerful way to identify the exciton character. By comparing the ab initio solution of the many-body Bethe-Salpeter equation for graphane and single-layer hexagonal boron nitride, we draw a general picture of the exciton dispersion in two-dimensional materials, highlighting the different role played by the exchange electron-hole interaction and by the electronic band structure. Our interpretation is substantiated by a prediction for phosphorene.

Estimating excitonic effects in the absorption spectra of solids: problems and insight from a guided iteration scheme.

A major obstacle for computing optical spectra of solids is the lack of reliable approximations for capturing excitonic effects within time-dependent density functional theory. We show that the accurate prediction of strongly bound electron-hole pairs within this framework using simple approximations is still a challenge and that available promising results have to be revisited. Deriving a set of analytical formulas we analyze and explain the difficulties. We deduce an alternative approximation from an iterative scheme guided by previously available knowledge, significantly improving the description of exciton binding energies. Finally, we show how one can "read" exciton binding energies from spectra determined in the random phase approximation, without any further calculation.

Dynamical effects in electron spectroscopy.

One of the big challenges of theoretical condensed-matter physics is the description, understanding, and prediction of the effects of the Coulomb interaction on materials properties. In electronic spectra, the Coulomb interaction causes a renormalization of energies and change of spectral weight. Most importantly, it can lead to new structures, often called satellites. These can be linked to the coupling of excitations, also termed dynamical effects. State-of-the-art methods in the framework of many-body perturbation theory, in particular, the widely used GW approximation, often fail to describe satellite spectra. Instead, approaches based on a picture of electron-boson coupling such as the cumulant expansion are promising for the description of plasmon satellites. In this work, we give a unified derivation of the GW approximation and the cumulant expansion for the one-body Green's function. Using the example of bulk sodium, we compare the resulting spectral functions both in the valence and in the core region, and we discuss the dispersion of quasi-particles and satellites. We show that self-consistency is crucial to obtain meaningful results, in particular, at large binding energies. Very good agreement with experiment is obtained when the intrinsic spectral function is corrected for extrinsic and interference effects. Finally, we sketch how one can approach the problem in the case of the two-body Green's function, and we discuss the cancellation of various dynamical effects that occur in that case.

Total Energy beyond GW: Exact Results and Guidelines for Approximations.

The total energy and electron addition and removal spectra can, in principle, be obtained exactly from the one-body Green's function (GF). In practice, the GF is obtained from an approximate self-energy. In the framework of many-body perturbation theory, we derive different expressions that are based on an approximate self-energy, but that yield nevertheless, in principle, the exact exchange-correlation contribution to the total energy for any interaction strength. Response functions play a crucial role, which explains why, for example, ingredients from time-dependent density functional theory can be used to build these approximate self-energies. We show that the key requirement for obtaining exact results is the consistent combination of ingredients. Also when further approximations are made, as it is necessary in practice, this consistency remains the key to obtain good results. All findings are illustrated using the exactly solvable symmetric Hubbard dimer.

Seed germination and vegetative and in vitro propagation of Hieracium lucidum subsp. lucidum (Asteraceae), a critically endangered endemic taxon of the Sicilian flora.

Hieracium lucidum subsp. lucidum is a critically endangered endemic taxa of the Sicilian flora. It is a relict of the Tertiary period surviving on the cliffs of Monte Gallo (NW-Sicily). This research focused on finding the best protocols for seed germination and vegetative and in vitro propagation to contribute to ex situ conservation. Seed germination tests were carried out using constant temperatures of 15 °C, 20 °C and 25 °C in continuous darkness and an alternating temperature of 30/15 °C (16 h/8 h, light/dark). The seeds had no dormancy, and a high germination capacity (70-95%) was obtained at all tested thermoperiods. The possibility of vegetative propagation of the taxon was evaluated through the rooting capacity of stem cuttings treated or not treated with indole-3-butyric acid (IBA). All cuttings were treated with IBA rooted within 2 months, while only 50% of the untreated cuttings were rooted within a longer time. An efficient protocol for rapid in vitro propagation from leaf portions was developed. The response of explants was tested on hormone-free Murashige and Skoog (MS) basal medium and MS enriched with different types of cytokinins: 6-Benzylaminopurine (BAP) and meta-Topolin (mT) in combination with naphthaleneacetic acid (NAA) and 2,4-Dichlorophenoxyacetic acid (2,4-D) at the same concentration. The combination of mT (2 mg L-1) and 2,4-D (1 mg L-1) in the medium was the most effective and showed the highest percentage of callus induction and the mean number of regenerated shoots. The maximum rate of root regeneration and the maximum number and length of roots were obtained on hormone-free MS and MS enriched with IBA at concentrations of 1 mg L-1. From the results obtained, it can be concluded that H. lucidum subsp. lucidum can be successfully propagated using one of the tested techniques, subject to the availability of the material for reproduction.

Micropropagation of Endemic Endangered Taxa of the Italian Flora: Adenostyles alpina subsp. macrocephala (Asteraceae), as a Case Study.

The conservation of endangered, rare, and endemic plant species is based on in situ and ex situ conservation strategies. When in situ conservation alone is not sufficient to guarantee the survival of the species, ex situ techniques are adopted in support. This study aimed to develop an efficient micropropagation protocol for Adenostyles by evaluating the effect of different plant growth regulators on leaf explants. Adenostyles alpina subsp. macrocephala (Asterace) is a perennial herbaceous plant endemic to Calabria (Southern Italy). The genus Adenostyles includes three species confined to the mountains of the Mediterranean and southern Europe. For callus induction, media supplemented with different concentrations of Benzylaminopurine (BAP) (0.5, 1, 2, and 3 mg L-1), Naphthaleneacetic Acid (NAA) (1 mg L-1), and 2,4-Dichlorophenoxyacetic Acid (2,4-D) (1 mg L-1) were tested. Shoot regeneration and proliferation were obtained in media supplemented with BAP (1, 2, and 3 mg L-1) and NAA (1 mg L-1). Root induction was obtained in media supplemented with IBA (0.25, 0.50, and 1 mg L-1) and NAA (0.25, 0.50, and 1 mg L-1). Statistically significant differences in callus induction and shoot regeneration were observed between the various media tested. The medium containing Murashige and Skoog (MS) supplemented with 3 mg L-1 of BAP and 1 mg L-1 of NAA showed the highest percentage of callus induction and increased shoot regeneration. The regenerated shoots showed more effective root induction in the hormone-free MS medium and in the presence of Indole-3-Butyric Acid (IBA) at concentrations of 0.25, 0.50, and 1 mg L-1. These results can be used as a basis for the preparation of a micropropagation protocol for different taxa of Adenostyles, as well as other species of Asteraceae specialized to the Mediterranean mountain habitat.

A New Bloody Pulp Selection of Myrobalan (Prunus cerasifera L.): Pomological Traits, Chemical Composition, and Nutraceutical Properties.

A new accession of myrobalan (Prunus cerasifera L.) from Sicily (Italy) was studied for the first time for its chemical and nutraceutical properties. A description of the main morphological and pomological traits was created as a tool for characterization for consumers. For this purpose, three different extracts of fresh myrobalan fruits were subjected to different analyses, including the evaluation of total phenol (TPC), flavonoid (TFC), and anthocyanin (TAC) contents. The extracts exhibited a TPC in the range 34.52-97.63 mg gallic acid equivalent (GAE)/100 g fresh weight (FW), a TFC of 0.23-0.96 mg quercetin equivalent (QE)/100 g FW, and a TAC of 20.24-55.33 cyanidine-3-O-glucoside/100 g FW. LC-HRMS analysis evidenced that the compounds mainly belong to the flavonols, flavan-3-ols, proanthocyanidins, anthocyanins, hydroxycinnamic acid derivatives, and organic acids classes. A multitarget approach was used to assess the antioxidant properties by using FRAP, ABTS, DPPH, and ß-carotene bleaching tests. Moreover, the myrobalan fruit extracts were tested as inhibitors of the key enzymes related to obesity and metabolic syndrome (α-glucosidase, α-amylase, and lipase). All extracts exhibited an ABTS radical scavenging activity that was higher than the positive control BHT (IC50 value in the range 1.19-2.97 µg/mL). Moreover, all extracts showed iron-reducing activity, with a potency similar to that of BHT (53.01-64.90 vs 3.26 µM Fe(II)/g). The PF extract exhibited a promising lipase inhibitory effect (IC50 value of 29.61 µg/mL).

Antibacterial activity and chemical characterization of almond (Prunus dulcis L.) peel extract.

In this study, almond skin of Prunus dulcis L. variety Casteltermini was characterised for its chemical composition and for the inhibitory activity towards food associated microorganisms belonging to pathogenic (Salmonella Enteritidis, Staphylococcus aureus, Escherichia coli and Listeria monocytgenes), spoilage (Pseudomonas poae and Brochotrix thermospacta) and useful (Levilactobacillus brevis and Saccharomyces cerevisiae) groups. The n-hexane extract of P. dulcis skin, investigated by GC-MS, evidenced linoleic, palmitic, and oleic acids as the main abundant compounds. Staphylococcus aureus ATCC 33862 growth was strongly limited by n-hexane extract and the minimum inhibition concentration (MIC) was 25.5 mg/mL. These results highlight the potential of almond by-products as food bio-preservatives as well as pharmaceutical products.

Chemical composition, antimicrobial, and antioxidant activities of Opuntia stricta (Haw.) Haw. mucilage collected in Sicily, Italy.

In this work the mucilage obtained from the cladodes of a not previously investigated accession of Opuntia stricta (Haw.) Haw. (syn. Opuntia dillenii (Ker-Gawl) Haw), collected in Sicily, was analysed by 13C-NMR. The yield of mucilage extracted from cladodes in aqueous medium was 2.55%. The monosaccharides identified, after acidic hydrolyses of the mucilage, were arabinose (36.48%), galactose (32.31%), xylose (15.33%), glucose (10.45%) and rhamnose (5.40%). The mucilage showed a sufficient antimicrobial activity and excellent antioxidant property.

Reuse of almond by-products: Functionalization of traditional semolina sourdough bread with almond skin.

Almond production generates large amounts of by-products rich in polyphenols. In this study, almond skin was explored as a valuable food ingredient in bread making. To this purpose, almond skin was used to produce functional products modifying a traditional sourdough bread recipe. The doughs were prepared replacing semolina with powdered almond skin (PAS) at 5 and 10 % (w/w). Sourdough inoculum was started with a mix of lactic acid bacteria (LAB) and propagated in semolina until reaching pH 3.7. The pH of PAS added breads was higher than that of control (CTR) breads before and after fermentation. Plate counts showed a similar evolution of LAB and total mesophilic microorganisms, but members of Enterobacteriaceae and coliform were detectable in PAS doughs. Illumina data clearly showed a dominance of lactobacilli in all trials, but PAS doughs displayed the presence of Bacillus. The final bread characteristics were influenced by PAS and its addition percentage; in particular, crust and crumb colour resulted darker, the alveolation decreased and, regarding sensory attributes, odour intensity increased, while bread odour diminished. In presence of PAS, bread emissions were characterized by lower percentages of alcohols and aromatic hydrocarbons and higher percentages of the other volatile compound classes, especially terpenoids like ß-pinene, ß-myrcene and limonene than CTR trial. After in vitro simulated digestion, the final release of phytochemicals from 10 % PAS bread was almost 100 %. Thus, PAS determined an increase of the antioxidant capacity of the breads. Phytochemicals released from digested PAS-fortified bread can provide antioxidant protection in a complex biological environment such as human intestinal-like cells. Besides the positive functional properties of PAS, this work also evidenced the hygienic issues of almond skin and, in order to avoid potential risks for the human health, highlighted the need to preserve its microbiological characteristics during storage for their reuse in bread production.

The Chemistry and the Anti-Inflammatory Activity of Polymethoxyflavonoids from Citrus Genus.

Polymethoxyflavonoids (PMFs) are a large group of compounds belonging to the more general class of flavonoids that possess a flavan carbon framework decorated with a variable number of methoxy groups. Hydroxylated polymethoxyflavonoids (HPMFs), instead, are characterized by the presence of both hydroxyl and methoxy groups in their structural unities. Some of these compounds are the aglycone part in a glycoside structure in which the glycosidic linkage can involve the -OH at various positions. These compounds are particular to Citrus genus plants, especially in fruits, and they are present mainly in the peel. A considerable number of PMFs and HPMFs have shown promising biological activities and they are considered to be important nutraceuticals, responsible for some of the known beneficial effects on health associated with a regular consumption of Citrus fruits. Among their several actions on human health, it is notable that the relevant contribution in controlling the intracellular redox imbalance is associated with the inflammation processes. In this work, we aim to describe the status concerning the chemical identification and the anti-inflammatory activity of both PMFs and HPMFs. In particular, all of the chemical entities unambiguously identified by isolation and complete NMR analysis, and for which a biochemical evaluation on the pure compound was performed, are included in this paper.

Ethnobotany, Phytochemistry, Biological, and Nutritional Properties of Genus Crepis-A Review.

The genus Crepis L., included within the Asteraceae family, has a very wide distribution, expanding throughout the northern hemisphere, including Europe, northern Africa, and temperate Asia. This genus has a fundamental value from biodynamic and ecological perspectives, with the different species often being chosen for soil conservation, for environmental sustainability, and for their attraction towards pollinating species. Furthermore, various species of Crepis have been used in the popular medicine of several countries as medicinal herbs and food since ancient times. In most cases, the species is consumed either in the form of a decoction, or as a salad, and is used for its cardiovascular properties, as a digestive, for problems related to sight, for the treatment of diabetes, and for joint diseases. This literature review, the first one of the Crepis genus, includes publications with the word 'Crepis', and considers the single metabolites identified, characterised, and tested to evaluate their biological potential. The various isolated compounds, including in most cases sesquiterpenes and flavonoids, were obtained by extracting the roots and aerial parts of the different species. The secondary metabolites, extracted using traditional (solvent extraction, column chromatography, preparative thin layer chromatography, preparative HPLC, vacuum liquid chromatography), and modern systems such as ultrasounds, microwaves, etc., and characterised by mono- and bi- dimensional NMR experiments and by HPLC-MS, have a varied application spectrum at a biological level, with antimicrobial, antioxidant, antidiabetic, antitumor, antiviral, antiulcer, phytotoxic, and nutritional properties having been reported. Unfortunately, in vitro tests have not always been accompanied by in vivo tests, and this is the major critical aspect that emerges from the study of the scientific aspects related to this genus. Therefore, extensive investigations are necessary to evaluate the real capacity of the different species used in food, and above all to discover what the different plants that have never been analysed could offer at a scientific level.

Dietary Patterns at the Individual Level through a Nutritional and Environmental Approach: The Case Study of a School Canteen.

The public catering sector has important responsibilities in seeking a change toward more sustainable choices for many aspects related to the environmental impacts of their services. The environmental impact of production processes can be studied through life cycle assessment (LCA), which allows a greater awareness of choices and has rarely been applied to catering. In this work, we studied the impacts of two dishes (braised meat and cauliflower meatballs) in a school canteen, their impacts were studied using the daily energy requirement (expressed in kcal) as a functional unit. Global warming potential (GWP) and nonrenewable energy (NRE) were calculated starting from the supply of raw materials up to distribution. Electricity and the act of cooking the meatballs accounted for more than 60% of the measured impact in terms of GWP, whereas, less markedly, they dominated in terms of nonrenewable energy used. In the case of braised meat, the total impact was, however, attributable to the life cycle of the meat (between 60% and 76%) and the consumption of electricity (between 19% and 27%), whereas for all other factors, the contribution was never particularly high. Additionally, a discussion on the correct functional unit to be used proposed the environmental impact of different recipes as an additional criterion for nutritionists during the composition of the menu. An integrated system appears important for changing policies and behaviors and the application of LCA can be a tool capable of contributing to the construction of a holistic instrument of sustainability.

Valence electron photoemission spectrum of semiconductors: ab initio description of multiple satellites.

The experimental valence band photoemission spectrum of semiconductors exhibits multiple satellites that cannot be described by the GW approximation for the self-energy in the framework of many-body perturbation theory. Taking silicon as a prototypical example, we compare experimental high energy photoemission spectra with GW calculations and analyze the origin of the GW failure. We then propose an approximation to the functional differential equation that determines the exact one-body Green's function, whose solution has an exponential form. This yields a calculated spectrum, including cross sections, secondary electrons, and an estimate for extrinsic and interference effects, in excellent agreement with experiment. Our result can be recast as a dynamical vertex correction beyond GW, giving hints for further developments.

Post-harvest Industrial Processes of Almond (Prunus dulcis L. Mill) in Sicily Influence the Nutraceutical Properties of By-Products at Harvest and During Storage.

Almond cultivation in Sicily is experiencing a phase of great interest which is mainly concentrated in the development of specialized orchards, with irrigation and by adopting cultivars with high qualitative and quantitative performances. These are mostly Mediterranean genotypes with high fat content and hard or semi-hard shell, extremely different from the varieties of Californian diffusion. The development of the sector comprises the primary production of almonds but also a series of secondary products which often represent a burden for the company. From these considerations several researches have been developed with the aim of giving a value to these by-products through circular economy paths. One of the by-products widely produced, besides the shell, is the skin which covers the seed and is produced during the peeling phase. It is well-known that tegument is an important component of almond because it contains important bioactive substances (phenols and aromas) which are usually dispersed during peeling. This paper examined three different Italian cultivars widely spread in Sicily, two of Apulian origin, (Genco and Tuono), and one locally cultivated variety (Vinci a tutti). These three cultivars occupy an increasingly large area and are very popular with consumers and industry. The production of secondary products, therefore, evidences significant quantities and the possibility to give them an added value becomes a need for the sector. Therefore, the content of phenols and proanthocyanins in the skin at harvest and during storage was analyzed, adopting two different separation methods, with and without water. During the analysis it was possible to observe the different behavior of the three cultivars due to genetic and industrial factors. Skin separated without using hot water showed a higher total phenolic presence with average increases of about 20%, and with even higher increases, between 28 and 32%, for proanthocyanins. Vinci a tutti evidenced the highest total phenolic content after 8 months of storing while roasting has revealed to be a more effective skin separation approach.