Mapping of two new markers within the smallest interval harboring the spinal muscular atrophy locus by family and radiation hybrid analysis

The locus responsible for the childhood-onset proximal spinal muscular atrophies (SMA) has recently been mapped to an area of 2–3 Mb in the region q12–13.3 of chromosome 5. We have used a series of radiation hybrids (RHs) containing distinct parts of the SMA region as defined by reference markers. A cosmid library was constructed from one RH. Thirteen clones were isolated and five of these were mapped within the SMA region. Both RH mapping and fluorescence in situ hybridization analysis showed that two clones map in the region between loci D5S125 and D5S351. One of the cosmids contains expressed sequences. Polymorphic dinucleotide repeats were identified in both clones and used for segregation analysis of key recombinant SMA families. One recombination between the SMA locus and the new marker 9Ic (D5S685) indicates that 9Ic is probably the closest distal marker. The absence of recombination between the SMA locus and marker Fc (D5S684) suggests that Fc is located close to the disease gene. These new loci should refine linkage analysis in SMA family studies and may facilitate the isolation of the disease gene.     

Effects of Sirolimus treatment on patients with β-Thalassemia: Lymphocyte immunophenotype and biological activity of memory CD4+ and CD8+ T cells

Inhibitors of the mammalian target of rapamycin (mTOR) have been proposed to improve vaccine responses, especially in the elderly. Accordingly, testing mTOR inhibitors (such as Sirolimus) and other geroprotective drugs might be considered a key strategy to improve overall health resilience of aged populations. In this respect, Sirolimus (also known as rapamycin) is of great interest, in consideration of the fact that it is extensively used in routine therapy and in clinical studies for the treatment of several diseases. Recently, Sirolimus has been considered in laboratory and clinical studies aimed to find novel protocols for the therapy of hemoglobinopathies (e.g. β-Thalassemia). The objective of the present study was to analyse the activity of CD4⁺ and CD8⁺ T cells in β-Thalassemia patients treated with Sirolimus, taking advantages from the availability of cellular samples of the NCT03877809 clinical trial. The approach was to verify IFN-γ releases following stimulation of peripheral blood mononuclear cells (PBMCs) to stimulatory CEF and CEFTA peptide pools, stimulatory for CD4⁺ and CD8⁺ T cells, respectively. The main results of the present study are that treatment of β-Thalassemia patients with Sirolimus has a positive impact on the biological activity and number of memory CD4⁺ and CD8⁺ T cells releasing IFN-γ following stimulation with antigenic stimuli present in immunological memory. These data are to our knowledge novel and in our opinion of interest, in consideration of the fact that β-Thalassemia patients are considered prone to immune deficiency.     

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 .     

Welcome aboard: are birds migrating across the Mediterranean Sea using ships as stopovers during adverse weather conditions?

Birds use stopovers during migration to interrupt endurance flight in order to minimize immediate and/or future fitness costs. Stopovers on ships is considered an exceptional and anecdotal event in the ornithological literature. This does not match the experience we had in the summer of 2021, during an oceanographic campaign in the Central Mediterranean, when we regularly observed on average 2.8 birds, of at least 13 species, stopping on board during the 25 days of the campaign. The median stopping time was 42 min, ranging from a few minutes to overnight stays on board. The probability of finding a bird stopping aboard increased with wind force and cloud cover. Birds also stopped more often in a headwind and did not stop when the wind came from different directions other than the headwind. The Central Mediterranean is one of the busiest sea routes in the world, combining the mean daily number of birds on board with the thousands of ships that pass through it during the 3 months of summer migration; we estimate that nearly 4 million birds could use ships as stopover sites. This behaviour may represent a modern-day strategy that uses ships as stopovers in the event of adverse weather conditions or could act as an ecological trap, increasing the mortality of migrants. This phenomenon deserves more research attention and further studies recording body condition and tagging of individuals on board would be informative.     

Computer simulation of antibody binding specificity

A Monte Carlo algorithm that searches for the optimal docking configuration of hen egg white lysozyme to an antibody is developed. Both the lysozyme and the antibody are kept rigid. Unlike the work of other authors, our algorithm does not attempt to explicitly maximize surface contact, but minimizes the energy computed using coarse-grained pair potentials. The final refinement of our best solutions using all-atom OPLS potentials (Jorgensen and Tirado-Rives⁸) consistently yields the native conformation as the preferred solution for three different antibodies. We find that the use of an exponential distance-dependent dielectric function is an improvement over the more commonly used linear form. © 1993 Wiley-Liss, Inc.     

Substitution of transferrin by FeCl3 in the development of a low foetal calf serum concentration medium for KB-26.5 hybridoma cell line

KB-26.5, a murine hybridoma cell line producing an IgG₃ monoclonal antibody used in blood type determination, primarily adapted to grow at 5% foetal calf serum (FCS) concentration has been adapted to grow at 0.5% FCS, maintaining its ability to produce antibodies at the same level. In the final step of adaptation, the addition of insulin, transferrin, ethanolamine and selenium to the media formulation was studied, using factorial assay techniques to check the effect of the different compounds and to optimize their required level for satisfactory growth and antibody secretion. KB-26.5 cells required only 20 g/ml of transferrin to adapt to 0.5% FCS medium. Furthermore, transferrin could be substituted by FeCl₃, at a relatively low level of 2 g/ml. Maximum cell density decreased by 31.5% in spinner flask test, but the antibody titer was maintained, thus the specific productivity increased. However, inoculum size had to be increased three-fold with 0.5% FCS medium in order to assure cell growth.     

TCEN-49, a monoclonal antibody that identifies a central body antigen in the planarian Dugesia (Girardia) tigrina. Implications for pattern formation and positional signalling mechanisms

We have produced monoclonal antibodies (mAbs) against antigens of the freshwater planarian Dugesia (G.) tigrina (Girard) using standard protocols. One of these mAbs, TCEN-49, detects an antigen (TCEN-49Ag) present in most cells of the central area of the body, including the pharynx. Labelled cells seem more related by position than by lineage, suggesting that TCEN-49Ag is involved somehow in the expression of central body positional identity. The spatial and temporal changes in TCEN-49Ag expression during growth/degrowth and regeneration have been monitored and the implications of these results are discussed.     

EFFECTS OF COMPETITION AND DISTURBANCE ON THE RESPROUTING PERFORMANCE OF THE MEDITERRANEAN SHRUB ERICA MULTIFLORA L. (ERICACEAE)

Two field experiments were designed to evaluate the importance of competition, fire, repeated disturbance, and their interactions on the vegetative and reproductive performance of the Mediterranean shrub Erica multiflora over a 2.5-yr period. In a burn experiment, fire was applied to the ground-level stumps of previously clipped 13-yr-old plants with a propane torch and competition was diminished by removal of neighboring plants. Fire resulted in a reduction of sprout vigor and biomass of flowers; mature neighbors also reduced E. multiflora sprout vigor and flowering. The interaction between fire and competition was nonsignificant. In a stand burned by a wildfire we studied the effects of regenerating neighbors on target plants by removing all neighbors or only Quercus coccifera, the most dominant species in the burned stand. In this stand we also simulated herbivory by repeatedly clipping the sprouts of E. multiflora. Regenerating neighbors did not affect target plant sprout vigor after the wildfire, but did cause a decrease in the biomass of flowers per plant. Survival decreased after repeated clipping but was not affected by neighborhood treatment. The results suggest that the importance of competition on resprouting vigor was temporally variable. Variables related to plant size rather than species determined competitive superiority: resprouting neighbors did not affect resprouting performance of target plants, but mature neighbors did. In nature, fire may directly reduce vegetative and reproductive biomass by the heating effect. But it may have an indirect positive effect on biomass, by reducing competition among plants. Frequent disturbances that removed aboveground biomass of E. multiflora had a detrimental effect on target plant survival independent of neighborhood effect.     

De novo missense mutation Y174S in exon 1 of the adrenoleukodystrophy (ALD) gene

Adrenoleukodystrophy (ALD) is an X-linked disease, characterised by an alteration of the peroxisomal -oxidation of the very long chain fatty acids. The ALD gene has been identified and mutations have been detected in ALD patients. We report here a new missense mutation in the ALD gene of a male patient, predicting a tyrosine to serine substitution at codon 174 (mutation Y174S). The mother of the ALD patient does not have the Y174S mutation in her leukocyte DNA, indicating that Y174S arose de novo in the patient. Y174S is the first reported de novo mutation in the ALD gene.     

Circadian organization in the ruin lizard Podarcis sicula: the role of the suprachiasmatic nuclei of the hypothalamus

The effects of electrolytic lesions to the suprachiasmatic nuclei of the hypothalamus (SCN) on circadian rhythms of locomotor activity were examined in ruin lizards Podarcis sicula maintained in constant darkness and constant temperature (29°C). All lizards (N=15) in which the lesion damaged 80% or more of the SCN became behaviorally arrhythmic. On the contrary, locomotor rhythms persisted in all cases (N=11) when the SCN remained intact and lesions were confined to neighbouring regions of the preoptic area. Taken together with previous work which demonstrates that the pineal and the retinae are not essential for the persistence of circadian locomotor rhythmicity in Podarcis sicula and with recent evidence showing the homology between the SCN of lizards and those of mammals the present results strongly support the view that the SCN of Podarcis sicula contain the primary pacemaker(s) for locomotor rhythms.Abbreviations DD constant darkness - LL constant light - SCN suprachiasmatic nuclei of the hypothalamus - PH nucleus periventricularis hypothalami - OC optic chiasm - te length of circadian activity - freerunning circadian period