Simulation of protein diffusion: a sensitive probe of protein–solvent interactions

Aqueous solutions of Candida antarctica lipase B (CALB) were simulated considering three different water models (SPC/E, TIP3P, TIP4P) by a series of molecular dynamics (MD) simulations of three different box sizes (L = 9, 14, and 19 nm) to determine the diffusion coefficient, the water viscosity and the protein density. The protein–water systems were equilibrated for 500 ns, followed by 100 ns production runs which were analysed. The diffusional properties of CALB were characterized by the Stokes radius (R_S), which was derived from the diffusion coefficient and the viscosity. R_S was compared to the geometric radius (R_G) of CALB, which was derived from the protein density. R_S and R_G differed by 0.27 nm for SPC/E and by 0.40 and 0.39 nm for TIP3P and TIP4P, respectively, which characterizes the thickness of the diffusive hydration layer on the protein surface. The simulated hydration layer of CALB resulted in agreement with those experimentally determined for other seven different proteins of comparable size. By avoiding the most common pitfalls, protein diffusion can be reliably simulated: simulating different box sizes to account for the finite size effect, equilibrating the protein–water system sufficiently, and using the complete production run for the determination of the diffusion coefficient.     

Stereotactic radiotherapy for brain oligometastases

Brain metastases, the most common metastases in adults, will develop in up to 40% of cancer patients, accounting for more than one-half of all intracranial tumors. They are most associated with breast and lung cancer, melanoma and, less frequently, colorectal and kidney carcinoma.Magnetic resonance imaging (MRI) is the gold standard for diagnosis. For the treatment plan, computed tomography (CT ) images are co-registered and fused with a gadolinium-enhanced T1-weighted MRI where tumor volume and organs at risk are contoured. Alternatively, plain and contrast-enhanced CT scans are co-registered. Single-fraction stereotactic radiotherapy (SRT ) is used to treat patients with good performance status and up to 4 lesions with a diameter of 30 mm or less that are distant from crucial brain function areas. Fractionated SRT (2–5 fractions) is used for larger lesions, in eloquent areas or in proximity to crucial or surgically inaccessible areas and to reduce treatment-related neurotoxicity. The single-fraction SRT dose, which depends on tumor diameter, impacts local control. Fractionated SRT may encompass different schedules. No randomized trial data compared the safety and efficacy of single and multiple fractions. Both single-fraction and fractionated SRT provide satisfactory local control rates, tolerance, a low risk of transient acute adverse events and of radiation necrosis the incidence of which correlated with the irradiated brain volume.     

Malcolmia littorea: The isolated Italian population in the European context

We compared the coenological information of the only Italian population of Malcolmia littorea (L.) R. Br. with published phytosociological relevés, including ones of this species, throughout its European range. With the aim of highlighting the main climatic features influencing the distribution patterns of M. littorea, we integrated coenological data with some climatic variables and considered major drivers for plant distribution at the European scale. Finally, we analysed the population extent of M. littorea in Italy, in order to assess its conservation status at regional level. The DCA analysis, performed on a matrix 139 relevés × 183 species, separated the relevés according to their floristic composition, showing a geographic gradient from Portugal to Mediterranean coasts, until Italy; with Mediterranean relevés clearly separated from Atlantic ones as well. Along the beach-inland gradient, the analysis highlights that the species is typical of fixed dunes habitats (more inland, mainly stabilised dunes), although in the Atlantic it can also be found in mobile dunes. The analysis of climatic variables in relation to M. littorea distribution, suggested that the species is sensitive to low winter temperature and to summer drought. The only Italian population of M. littorea is subjected to many threats, due to its small dimensions (<1 ha), isolation from the rest of its distribution area, that ranges from Portugal to France (until the Camargue region) and intensive human disturbances. Using both field and remote sensing information, we showed a considerable decrease of the occupied surface in Italy, leading us to suggest that the IUCN threat category of M. littorea in Italy should be reassessed from endangered to critically endangered.     

A molecular phylogeny of antarctic chironomidae and its implications for biogeographical history

The chironomid midges Belgica antarctica, Eretmoptera murphyi (subfamily Orthocladiinae) and Parochlus steinenii (subfamily Podonominae), are the only Diptera species currently found in Antarctica. The relationships between these species and a range of further taxa of Chironomidae were examined by sequencing domains 1 and 3–5 of 28S ribosomal RNA. The resulting molecular relationships between B. antarctica and E. murphyi, within Orthocladiinae, were highly supported by validation analyses, confirming their position within Chironomidae, as generated by classical taxonomy. Within Podonominae, P. steinenii from the Maritime Antarctic was more closely related to material from sub-Antarctic South Georgia than to material from Patagonia. Taking advantage of the availability of a molecular substitution rate calculated for this gene in Diptera, a dating of divergence between our study taxa was tentatively established. The divergence dates obtained were 49 million years (Myr), between B. antarctica and E. murphyi, and 68.5 Myr between these species and the closest Orthocladiinae taxon tested from Patagonia, suggesting that B. antarctica and E. murphyi were representatives of an ancient lineage. As both are endemic to their respective tectonic microplates, their contemporary distribution is, therefore, likely to have been shaped by vicariance rather than dispersal.     

Study of Adhesion and Survival of Lactobacilli and Bifidobacteria on Table Olives with the Aim of Formulating a New Probiotic Food

With the aim of developing new functional foods, a traditional product, the table olive, was used as a vehicle for incorporating probiotic bacterial species. Survival on table olives of Lactobacillus rhamnosus (three strains), Lactobacillus paracasei (two strains), Bifidobacterium bifidum (one strain), and Bifidobacterium longum (one strain) at room temperature was investigated. The results obtained using a selected olive sample demonstrated that bifidobacteria and one strain of L. rhamnosus (Lactobacillus GG) showed a good survival rate, with a recovery of about 10⁶ CFU g⁻¹ after 30 days. The Lactobacillus GG population remained unvaried until the end of the experiment, while a slight decline (to about 10⁵ CFU g⁻¹) was observed for bifidobacteria. High viability, with more than 10⁷ CFU g⁻¹, was observed throughout the 3-month experiment for L. paracasei IMPC2.1. This strain, selected for its potential probiotic characteristics and for its lengthy survival on olives, was used to validate table olives as a carrier for transporting bacterial cells into the human gastrointestinal tract. L. paracasei IMPC2.1 was recovered from fecal samples in four out of five volunteers fed 10 to 15 olives per day carrying about 10⁹ to 10¹⁰ viable cells for 10 days.     

Challenges for simultaneous nitrification, denitrification, and phosphorus removal in microbial aggregates: mass transfer limitation and nitrous oxide production

The microbial community composition and activity was investigated in aggregates from a lab-scale bioreactor, in which nitrification, denitrification and phosphorus removal occurred simultaneously. The biomass was highly enriched for polyphosphate accumulating organisms facilitating complete removal of phosphorus from the bulk liquid; however, some inorganic nitrogen still remained at the end of the reactor cycle. This was ascribed to incomplete coupling of nitrification and denitrification causing NO(3)(-) accumulation. After 2 h of aeration, denitrification was dependent on the activity of nitrifying bacteria facilitating the formation of anoxic zones in the aggregates; hence, denitrification could not occur without simultaneous nitrification towards the end of the reactor cycle. Nitrous oxide was identified as a product of denitrification, when based on stored PHA as carbon source. This observation is of critical importance to the outlook of applying PHA-driven denitrification in activated sludge processes.     

Specific protein changes contribute to the differential muscle mass loss during ageing

In the skeletal muscle, the ageing process is characterized by a loss of muscle mass and strength, coupled with a decline of mitochondrial function and a decrease of satellite cells. This profile is more pronounced in hindlimb than in forelimb muscles, both in humans and in rodents. Utilizing light and electron microscopy, myosin heavy chain isoform distribution, proteomic analysis by 2D‐DIGE, MALDI‐TOF MS and quantitative immunoblotting, this study analyzes the protein levels and the nuclear localization of specific molecules, which can contribute to a preferential muscle loss. Our results identify the molecular changes in the hindlimb (gastrocnemius) and forelimb (triceps) muscles during ageing in rats (3‐ and 22‐month‐old). Specifically, the oxidative metabolism contributes to tissue homeostasis in triceps, whereas respiratory chain disruption and oxidative‐stress‐induced damage imbalance the homeostasis in gastrocnemius muscle. High levels of dihydrolipoyllysine‐residue acetyltransferase (Dlat) and ATP synthase subunit alpha (Atp5a1) are detected in triceps and gastrocnemius, respectively. Interestingly, in triceps, both molecules are increased in the nucleus in aged rats and are associated to an increased protein acetylation and myoglobin availability. Furthermore, autophagy is retained in triceps whereas an enhanced fusion, decrement of mitophagy and of regenerative potential is observed in aged gastrocnemius muscle.