RosettaDDGPrediction for high-throughput mutational scans: From stability to binding

Reliable prediction of free energy changes upon amino acid substitutions (ΔΔGs) is crucial to investigate their impact on protein stability and protein–protein interaction. Advances in experimental mutational scans allow high-throughput studies thanks to multiplex techniques. On the other hand, genomics initiatives provide a large amount of data on disease-related variants that can benefit from analyses with structure-based methods. Therefore, the computational field should keep the same pace and provide new tools for fast and accurate high-throughput ΔΔG calculations. In this context, the Rosetta modeling suite implements effective approaches to predict folding/unfolding ΔΔGs in a protein monomer upon amino acid substitutions and calculate the changes in binding free energy in protein complexes. However, their application can be challenging to users without extensive experience with Rosetta. Furthermore, Rosetta protocols for ΔΔG prediction are designed considering one variant at a time, making the setup of high-throughput screenings cumbersome. For these reasons, we devised RosettaDDGPrediction, a customizable Python wrapper designed to run free energy calculations on a set of amino acid substitutions using Rosetta protocols with little intervention from the user. Moreover, RosettaDDGPrediction assists with checking completed runs and aggregates raw data for multiple variants, as well as generates publication-ready graphics. We showed the potential of the tool in four case studies, including variants of uncertain significance in childhood cancer, proteins with known experimental unfolding ΔΔGs values, interactions between target proteins and disordered motifs, and phosphomimetics. RosettaDDGPrediction is available, free of charge and under GNU General Public License v3.0, at https://github.com/ELELAB/RosettaDDGPrediction .     

Immunological responses in patients with tuberculosis and in vivo effects of acetyl-L-carnitine oral administration

Tuberculosis (TBC) is characterized by a complex immune response which parallels the clinical course of the disease. In this respect, acquired resistance, delayed hypersensitivity reaction and anergy are the main types of immune reactivity to mycobacterial antigens. In view of the presence of nonspecific and specific immune deficits in TBC patients, a clinical trial was carried out in a group of 20 individuals with active pulmonary TBC by oral administration of acetyl-L-carnitine (ALC). This drug, which has been shown to possess immunomodulating activities, was able to upregulate the T-dependent antibacterial activity in TBC patients after 30 days' treatment, while the same activity decreased in patients receiving placebo only. On the other hand, ALC did not modify serum levels of tumour necrosis factor-alpha, in the same individuals. This cytokine plays a detrimental rather than beneficial role in TBC pathogenesis. In the light of these data, ALC seems to be a powerful immunomodulator in the course of Mycobacterium tuberculosis infection and other mycobacteriosis.     

Genetic variation in the Y chromosome and sex-biased DNA methylation in somatic cells in the mouse

Mammalian Genome - Several lines of evidence suggest that the presence of the Y chromosome influences DNA methylation of autosomal loci. To better understand the impact of the Y chromosome on...     

Heterogeneity in the mouse epidermal cell cycle analysed by computer simulations

Abstract. Different sets of cell kinetic data obtained over many years from hairless mouse epidermis have been simulated by a mathematical model including circadian variations. Simulating several independent sets of data with the same mathematical model strengthens the validity of the results obtained. The data simulated in this investigation were all obtained with the experimental system in a state of natural synchrony. The data include cell cycle phase distributions measured by DNA flow cytometry of isolated epidermal basal cells, fractions of tritiated thymidine ([³H]TdR) labelled cells within the cell cycle phases measured by cell sorting at intervals after [³H]TdR pulse labelling, bivariate bromodeoxyuridine (BrdUrd)/DNA data from epidermal basal cells isolated at intervals after pulse labelling with BrdUrd, mitotic rate and per cent labelled mitosis (PLM) data from histologic sections. The following main new findings were made from the simulations: the second PLM peak observed at about 35 h after pulse labelling is hardly influenced by circadian variations; the peak is mainly determined by persisting synchrony of a rapidly cycling population with a G₁-duration (T_G1) of 20 h to 30 h; and there is a highly significant population of slowly cycling G₁-cells (G_1σ). However, no significant circadian variations were found in the number of these cells.     

Plenty of rooftops with few neighbours occupied by young breeding Yellow-legged Gulls (Larus michahellis): Does this occur at the expense of their health condition?

Gulls, as largely flexible opportunistic individuals, have been increasingly breeding in many cities around the world, but it is still unclear whether urban habitats are of equal or higher quality than traditional natural habitats or represent an ecological trap with immediate reproductive benefits but longer-term detrimental consequences to health. Here we present a study of breeding parameters (nest density, egg dimensions, clutch size, hatching success and adult body condition) and physiological parameters (erythrocyte sedimentation rate, heterophil/lymphocyte ratio, haemoglobin concentration and measurements of oxidative stress) as indicators of the general health condition of Yellow-legged Gull Larus michahellis adults and chicks from natural and urban colonies. Yellow-legged Gulls in the largest urban area (Porto) laid smaller eggs and clutches, showed a significantly lower occurrence of inflammatory processes in chicks, and showed a slower early chick growth than in the natural colony of Deserta. This suggests that urban gulls might be facing important trade-offs between the advantages of breeding in lower density urban colonies, with fewer intraspecific interactions and a lower disease transmission probability, and the disadvantages of having an anthropogenic diet usually lower in nutritional value.     

Population genetic structure,parasite infection and somatic condition of pumpkinseed Lepomis gibbosus (Actinopterygii: Centrarchidae) in the Oder river basin

In Poland, distribution of non-native pumpkinseed Lepomis gibbosus (Centrarchidae) is strictly limited to the Oder river basin, where it was introduced in the early 20th century. Recently, several populations have been found in waterbodies adjacent to the Oder, particularly in its lower reaches. In this study, we compare the genetic relatedness of populations in the Oder basin with other European populations using nuclear (microsatellite) and mitochondrial (partial cytochrome c oxidase subunit I; cox1) markers. Microsatellite analysis indicated that four populations in the lower Oder form a separate cluster, while one in the middle Oder clustered with Danubian populations, from where probably having been introduced. Microsatellite data suggested that the lower Oder populations differ from other non-native European populations, making it impossible to estimate the source of introduction. Nevertheless, analysis of cox1 indicated that Oder pumpkinseeds belong to the same haplotype as the vast majority of European populations. Parasitological examination confirmed the presence of two North American species, the monogenean Onchocleidus dispar and trematode Posthodiplostomum centrarchi, in the lower Oder, both previously unknown in the region. Fifteen other parasite species were acquired, including glochidia of invasive Sinanodonta woodiana. In the middle Oder, parasite infection was more limited. Fish from the Gryfino Canal, considered one of the most invasive populations in Europe, showed the highest parasite abundance and diversity, and the highest somatic condition and growth rate due to warm water released from the Dolna Odra power plant. Our results highlight significant differences in somatic condition and parasite infection in long-established non-native pumpkinseed populations in the same river system, reflecting mainly environmental conditions.     

Trophic ecology of juvenile bull sharks (Carcharhinus leucas) in the Coyote estuary,Costa Rica

Bull shark (Carcharhinus leucas) is a near-threatened elasmobranch species capable of moving between the fresh and salty waters of tropical and subtropical coastal areas, for which we still lack important ecological information. During their first years of life, bull sharks use estuarine systems as nursery areas, making them highly susceptible to environmental and anthropogenic pressures. We studied the trophic ecology of juveniles found in the Coyote estuary, a potential nursery area in Costa Rica, to understand the potential impact of further bull shark declines and gain knowledge that could aid in their conservation. We analysed the trophic ecology of juvenile bull sharks [81–103 cm total length (TL)] in the Coyote estuary, Costa Rica, using stable isotopes of δ¹⁵N and δ¹³C. Since one problem using this technique in juveniles is the confounding effect of the maternal signature, we sampled different tissues (muscle and plasma), verified the status of the shark's umbilical scar and identified the size at which the isotope signature is a result of the animal's current diet. The isotopic values of the muscle tissue reflected the maternal isotopic signature. In contrast, plasma values reflected the diet of juvenile bull sharks >95 cm TL and with a closed umbilical scar. Juvenile bull sharks fed primarily on teleost fishes of the order Anguilliformes and Siluriformes, and have a high trophic position (≥4.0) in the Coyote estuary. Our findings suggest that this estuary is an important feeding site for juvenile bull sharks of the Pacific of Costa Rica. Thus, the protection of essential habitats such as the Coyote estuary will benefit not only bull shark conservation, but also the conservation of an array of fish species that also use this habitat as a rookery, many of which are of commercial interest.     

Influences of sea level changes and volcanic eruptions on Holocene vegetation in Tonga

Here, we investigate Mid- to Late-Holocene vegetation changes in low-lying coastal areas in Tonga and how changing sea levels and recurrent volcanic eruptions have influenced vegetation dynamics on four islands of the Tongan archipelago (South Pacific). To investigate past vegetation and environmental change at Ngofe Marsh (‘Uta Vava’u), we examined palynomorphs (pollen and spores), charcoal (fire), and sediment characteristics (volcanic activity) from a 6.7-m-long sediment core. Radiocarbon dating indicated the sediments were deposited over the last 7700 years. We integrated the Ngofe Marsh data with similar previously published data from Avai’o’vuna Swamp on Pangaimotu Island, Lotofoa Swamp on Foa Island, and Finemui Swamp on Ha’afeva Island. Plant taxa were categorized as littoral, mangrove, rainforest, successional/ disturbance, and wetland groups, and linear models were used to examine relationships between vegetation, relative sea level change, and volcanic eruptions (tephra). We found that relative sea level change has impacted vegetation on three of the four islands investigated. Volcanic eruptions were not identified as a driver of vegetation change. Rainforest decline does not appear to be driven by sea level changes or volcanic eruptions. From all sites analyzed, vegetation at Finemui Swamp was most sensitive to changes in relative sea level. While vegetation on low-lying Pacific islands is sensitive to changing sea levels, island characteristics, such as area and elevation, are also likely to be important factors that mediate specific island responses to drivers of change.     

Revealing the polar lipidome,pigment profiles,and antioxidant activity of the giant unicellular green alga,Acetabularia acetabulum

Marine algae are one of the most important sources of high-value compounds such as polar lipids, omega-3 fatty acids, photosynthetic pigments, or secondary metabolites with interesting features for different niche markets. Acetabularia acetabulum is a macroscopic green single-celled alga, with a single nucleus hosted in the rhizoid. This alga is one of the most studied dasycladalean species and represents an important model system in cell biology studies. However, its lipidome and pigment profile have been overlooked. Total lipid extracts were analyzed using hydrophilic interaction liquid chromatography-high resolution mass spectrometry (HILIC-HRMS), tandem mass spectrometry (MS/MS), and high-performance liquid chromatography (HPLC). The antioxidant capacity of lipid extracts was tested using DPPH and ABTS assays. Lipidomics identified 16 polar lipid classes, corresponding to glycolipids, betaine lipids, phospholipids, and sphingolipids, with a total of 191 lipid species, some of them recognized by their bioactivities. The most abundant polar lipids were glycolipids. Lipid classes less studied in algae were identified, such as diacylglyceryl-carboxyhydroxymethylcholine (DGCC) or hexosylceramide (HexCer). The pigment profile of A. acetabulum comprised carotenoids (17.19%), namely cis-neoxanthin, violaxanthin, lutein and β,β-carotene, and chlorophylls a and b (82.81%). A. acetabulum lipid extracts showed high antioxidant activity promoting a 50% inhibition (IC₅₀) with concentrations of 57.91 ± 1.20 μg · mL⁻¹ (438.18 ± 8.95 μmol Trolox · g⁻¹ lipid) in DPPH and 20.55 ± 0.60 μg · mL⁻¹ in ABTS assays (918.56 ± 27.55 μmol Trolox · g⁻¹ lipid). This study demonstrates the potential of A. acetabulum as a source of natural bioactive molecules and antioxidant compounds.