The question about the stability of certain biomolecules is directly connected to the life-detection missions aiming to search for past or present life beyond Earth. The extreme conditions experienced on extraterrestrial planet surface (e.g. Mars), characterized by ionizing and non-ionizing radiation, CO2-atmosphere and reactive species, may destroy the hypothetical traces of life. In this context, the study of the biomolecules behaviour after ionizing radiation exposure could provide support for the onboard instrumentation and data interpretation of the life exploration missions on other planets. Here, as a part of STARLIFE campaign, we investigated the effects of gamma rays on two classes of fungal biomolecules–nucleic acids and melanin pigments – considered as promising biosignatures to search for during the ‘in situ life-detection’ missions beyond Earth.

Pathogenic helminth infections are responsible for severe health problems and economic losses worldwide. Timely and accurate diagnosis of helminth infections is critical for adopting suitable strategies for pathogen control. Here, we review recent advances in nucleic acid-based diagnostic methods, including polymerase chain reaction, quantitative qPCR, loop-mediated isothermal amplification and recombinase polymerase amplification, and discuss their advantages and disadvantages for diagnosing helminth infections. In addition, we highlight recent advances in biosensors for the detection of nucleic acid biomarkers that can potentially be used for the diagnosis of helminth infection.

To date, no structural study has been carried out on the effects of vitamin A deficiency (VAD) on hippocampal macromolecules. Therefore, in the present study, the effect of dietary VAD on the structure, content and function of rat hippocampal molecules was investigated using Fourier transform IF spectroscopy. Male Wistar rats were randomly divided into three groups: an experimental group maintained on a vitamin A-deficient liquid diet (VAD, n 7); a control group maintained on a vitamin A-supplemented liquid diet (CON, n 9); a pure control group maintained on standard solid laboratory chow (PC, n 7). The PC group was included in the study to ensure that the usage of liquid diet did not influence the outcomes of VAD. Both the CON and PC groups were successfully discriminated from the VAD group by principal component analysis and hierarchical cluster analysis. The spectral analysis indicated a significant decrease in the contents of saturated and unsaturated lipids, cholesteryl esters, TAG and nucleic acids in the VAD group when compared with the CON group (P≤ 0·05). In addition, a significant decrease in membrane fluidity and a significant increase in lipid order (e.g. acyl chain flexibility) were observed in the VAD group (P≤ 0·001). The results of the artificial neural network analysis revealed a significant decrease in the α-helix structure content and a significant increase in the turn and random coil structure contents, indicating protein denaturation, in the VAD group when compared with the CON and PC groups (P≤ 0·05). Dietary exclusion of vitamin A for 3 months apparently had an adverse impact on compositional, structural and dynamical parameters. These changes can be due to increased oxidative stress, confirming the antioxidant protection provided by vitamin A when used as a dietary supplement at low-to-moderate doses.

Decontamination of egg shells is required to improve the microbiological safety of the fresh hen eggs used for human consumption or for hatching. Conventional chemical decontamination methods involving quaternary ammonium disinfectant, sodium hydroxide, phenol, hydrogen peroxide or formaldehyde, leave residues on egg shells that may damage the cuticle layer. Therefore new techniques of egg shells decontamination, such as ultraviolet (UV) radiation, have been developed. This review aims to evaluate the data from available literature and to provide a general review of UV light treatment application for egg shell decontamination. Data shows that UV treatment was effective for the inactivation of the bacterial population present on clean egg shells and recently contaminated shells. Combined treatments such as UV light with ozone or hydrogen peroxide (H2O2) improved the inactivation of microorganisms. Recent advances in science and engineering indicate that treatment with UV light has a competitive advantage in comparison with traditional egg shell sanitation treatments for decontamination.

The conventional Poisson-Nernst-Planck equations do not account for the finite size of ions explicitly. This leads to solutions featuring unrealistically high ionic concentrations in the regions subject to external potentials, in particular, near highly charged surfaces. A modified form of the Poisson-Nernst-Planck equations accounts for steric effects and results in solutions with finite ion concentrations. Here, we evaluate numerical methods for solving the modified Poisson-Nernst-Planck equations by modeling electric field-driven transport of ions through a nanopore. We describe a novel, robust finite element solver that combines the applications of the Newton’s method to the nonlinear Galerkin form of the equations, augmented with stabilization terms to appropriately handle the drift-diffusion processes.

To make direct comparison with particle-based simulations possible, our method is specifically designed to produce solutions under periodic boundary conditions and to conserve the number of ions in the solution domain. We test our finite element solver on a set of challenging numerical experiments that include calculations of the ion distribution in a volume confined between two charged plates, calculations of the ionic current though a nanopore subject to an external electric field, and modeling the effect of a DNA molecule on the ion concentration and nanopore current.

Analysis of the major biochemical components of Taenia hydatigena cysticerci collected from goats and pigs showed marked differences, particularly in glycogen, protein, lipid and DNA levels. Differences were also detected in the levels of cholesterol, triglycerides, free fatty acids and phospholipids. Furthermore, the profile of phospholipid fractions revealed quantitative differences between the two species. It is concluded that the cysticerci of goat and pig origin probably represent two different strains and possibly follow the same pattern of speciation as reported in the related taeniid, Echinococcus granulosus.

Human milk is a rich source of RNA, free nucleotides (NT) and nucleosides (NS). To determine the uptake of different NS sources by the intestinal epithelium, jejunal explants from suckling piglets were cultured in a medium supplemented with a mixture of NS (adenosine, cytidine, guanosine, inosine, uridine; 10 mg/l each), a mixture of five NT (AMP, CMP, GMP, IMP, UMP; 7 mg/l each) or RNA (60 mg/l), respectively. Aliquots from the media were taken at different times (0·5, 2, 5, 15, 30, 60, 180 min). NS and NT concentrations were analysed in the different supernatants at those periods using solid-phase extraction followed by HPLC. When explants were cultured in the presence of NS the concentration of these compounds, excepting cytidine, rapidly decreased, suggesting that they are efficiently taken up. When explants were incubated in the presence of NT, the total concentration of these compounds decreased while the total concentration of NS increased, suggesting that enterocytes efficiently hydrolyse NT into NS. Likewise, when explants were incubated in the presence of RNA, the total concentration of both NT and NS increased, indicating that intestinal explants are able to hydrolyse RNA to NT and then to NS in the absence of luminal enzymes. In conclusion, the jejunum of piglets at weaning is able to hydrolyse RNA and free NT to NS, and NS, excepting cytidine, are efficiently taken up by the small intestine. These results suggest that the current concentration of NT used to supplement infant formulas should be reconsidered.

The process of catalysis of biochemical reactions has been essential since the first organic molecules appeared on Earth. As the complexity of the ensemble of primitive biomolecules was very low, primitive catalysts had necessarily to be very simple molecules or ions. The evolution of catalysts had to be in parallel with the evolution of the molecular species reacting. An example of this parallel evolution is nucleic acid polymerization. Synthesis of primitive short oligonucleotides could have been catalysed by metal ions either in solution or on the surface of minerals such as montmorillonite clays. Some oligonucleotides could start to function as templates for the synthesis of complementary copies and there is experimental evidence supporting the role also played by metal ions in this process. In later stages of evolution, a group of enzymatic proteins, nucleic acid polymerases, has been selected to catalyse nucleic acid replication. The presence of Mg2+ in the active centre of these enzymes suggests that evolution has preserved some of the primitive catalysts, including them as cofactors of more complex molecules. However, the reasons why Mg2+ was selected among other ions that possibly were present in primitive environments are unknown. In this paper we try to approach this question by analysing the amplification efficiency of the polymerase chain reaction of a DNA fragment in the presence of different metal ions. In some cases the conditions of the reaction have been displaced from optimum (by the presence of nucleotide imbalances and a suboptimal Mg2+concentration). The results obtained permit one to draw interesting conclusions about how some metallic cations can help replication to proceed in conditions of limited substrate availability, a circumstance that could have been frequent at prebiotic stages, when nucleic acid synthesis was dependent on the physico-chemical conditions of the environment.

Seasonal changes in nucleic acid concentrations and amino acid profiles in the muscle of juvenile Aristeus antennatus were investigated. RNA content, RNA:DNA and RNA:protein ratios varied significantly between seasons (p < 0.05), being the lowest and the highest values obtained in winter and spring/summer. A significant variation in the total amino acid content (TAA) from winter to summer was observed (p < 0.05). In fact, during this period a significant percent of increase in total non- (NEAA; 20.2%) and essential amino acids (EAA, 18.7%) contents occurred. Concomitantly, a significant decrease in the free amino acid (FAA) content from winter to summer was observed. A higher percentage of decrease with free essential amino acids (FEAA; 56.6%) in comparison to free non-essential amino acids (FNEAA; 34.2%) was attained. The significant increase in RNA and TAA contents from winter to summer may be related with protein synthesis. On the other hand, the lowest values obtained in winter may be due to a reduction in feeding activity; in this period the muscle protein must be progressively hydrolysed, which is evident with the higher FAA content. The liberated amino acids enter FAA pool and become available for energy production.

Drying of cells leads to damage resulting from crowding of cytoplasmic components, condensation of the nucleoid, increases in the Tm of membrane phase transitions, and imposition of stress upon cell walls. Prolonged desiccation leads to oxidation of proteins, DNA and membrane components through metal-dependent Fenton reactions, while Maillard reactions generate cross-linked products between the carbonyl groups of reducing sugars and the primary amines of nucleic acids and proteins. Although such damage restricts many organisms to aqueous environments, some, including many cyanobacteria, can tolerate the air-dried state for prolonged periods. Cyanobacteria in the Tintenstrich communities of exposed rock faces, Microcoleus and Lyngbya spp. in intertidal mats, chasmoendolithic Chroococcidiopsis spp. in the rocks of hot and cold deserts, and terrestrial epilithic crusts of Tolypothrix and Nostoc are examples that show a marked capacity to withstand the removal of their cellular water. For Nostoc commune, the mechanisms of desiccation tolerance reflect both simple and complex interactions at the structural, physiological and molecular levels.

An RNA spin-labeling technique was developed using the well-characterized interaction between the HIV Rev peptide and the Rev response element (RRE) RNA as a model system. Spin-labeled RNA molecules were prepared by incorporating guanosine monophosphorothioate (GMPS) at the 5′ end using T7 RNA polymerase and then covalently attaching a thiol-specific nitroxide spin label. Three different constructs of the RRE RNA were made by strategically displacing the 5′ end within the native three-dimensional structure. Nitroxide-to-nitroxide distance measurements were made between the specifically bound RNA and peptide using electron paramagnetic resonance (EPR) spectroscopy. The dipolar EPR method can reliably measure distances up to 25 Å, the calculation of which is derived from the 1/r3 dependence of the broadening of EPR lines in motionally frozen samples. This RNA-labeling technique, dubbed 5′ displacement spin labeling, extends the usefulness of the dipolar EPR method developed for analysis of protein structure. The advantage of this technique is that it is applicable to large RNA systems such as the ribosome, which are difficult to study by other structural methods.

The U1A protein binds to a hairpin RNA and an internal-loop RNA with picomolar affinities. To probe the molecular basis of U1A binding, we performed state-of-the-art nanosecond molecular dynamics simulations on both complexes. The good agreement with experimental structures supports the protocols used in the simulations. We compare the dynamics, hydrogen-bonding occupancies, and interfacial flexibility of both complexes and also describe a rigid-body motion in the U1A–internal loop complex that is not observed in the U1A–hairpin simulation. We relate these observations to experimental mutational studies and highlight their significance in U1A binding affinity and specificity.

In the course of evolving variants of the Tetrahymena thermophila Group I ribozyme for improved DNA cleavage in vitro, we witnessed the unexpected emergence of a derived molecular species, capable of acting as a partner for the ribozyme, but no longer autocatalytic. This new RNA species exhibits a deletion in the catalytic core and participates in a productive intermolecular interaction with an active ribozyme, thus insuring its survival in the population. These novel RNA molecules have evolved a precise catalytic interaction with the Group I ribozyme and depend for their survival on the continued presence of active catalysts. This interaction hints at the complexity that may inevitably arise even in simple evolving systems.

The present study examined the relationship between the supply of exogenous nucleic acid (NA) purines and their recovery as the derivatives hypoxanthine, xanthine, uric acid and allantoin in urine. Six lambs, totally nourished by intragastric infusions of volatile fatty acids (VFA) and casein (i.e. no rumen fermentation), were given by abomasal infusion a microbial NA concentrate at six levels (from zero to 24·5 mmol purines/d). The true digestibility between the abomasum and terminal ileum of the NA purines was measured in a separate experiment using three lambs. The relative proportion of urinary allantoin increased, and that of other derivatives decreased, as the amount of NA infused was increased. The relationship between total excretion of purine derivatives (Y; mmol/d) and exogenous purines absorbed (X; mmol/d) was Y = 0·84 X + 0.150W0·75e-0.25X, where W is body-weight (kg). This implies that the endogenous contribution to the total excretion of derivative decreased as the supply of exogenous purines increased, with an associated progressive replacement of de novo synthesis by exogenous purines. The model also implies that 0·16 of the purines were eliminated through routes other than derivative excretion in urine. Once excretion exceeded 0·6 mmol/kg W0·75 per d, endogenous excretion was effectively zero and thus Y = 0·84 X. In normally fed sheep, derivative excretion should therefore relate to the microbial purines and, hence, microbial protein absorbed according to these models. The changing proportions of allantoin and other derivatives in urine were probably due to changes in the relative importance of endogenous and exogenous purines as precursors.

The fat body protein content of silkworms increased with 0.5 μg of thyroxine (T4) per gram of body weight and more so with 1 μg/g on days 4 and 8 after injection. Thyroxine with 1 μg/g dose, however, caused an earlier increase in protein content on day 2. The higher doses of T4 (2 and 5 μg/g) decreased the protein content. All T4 treated groups (except with an ineffective dose of 0.25 μg/g) showed reduced protein level in the adult stage in comparison to the control. Thyroxine with a dose of 0.25, 0.5 and 1 μg/g increased the fat body RNA content over the control level which was observed on days 2, 4 and 8. But on day 13, the RNA content in these groups returned to the control level. Higher doses of T4 (2 and 5 μg/g) decreased the RNA content during the developmental period. DNA content was not altered by lower doses of T4 (0.25,0.5 and 1 μg/g), while the higher doses (2 and 5 μg/g) surprisingly caused a reduction in DNA content during the larval, pupal and adult stages.

The increase in protein and RNA contents with lower doses of T4 and decrease with higher doses, indicates a biphasic nature of thyroid hormone action in silkworm fat body.