SASBDB: Towards an automatically curated and validated repository for biological scattering data

Small‐angle scattering (SAS) of X‐rays and neutrons is a fundamental tool to study the nanostructural properties, and in particular, biological macromolecules in solution. In structural biology, SAS recently transformed from a specialization into a general technique leading to a dramatic increase in the number of publications reporting structural models. The growing amount of data recorded and published has led to an urgent need for a global SAS repository that includes both primary data and models. In response to this, a small‐angle scattering biological data bank (SASBDB) was designed in 2014 and is available for public access at www.sasbdb.org . SASBDB is a comprehensive, free and searchable repository of SAS experimental data and models deposited together with the relevant experimental conditions, sample details and instrument characteristics. SASBDB is rapidly growing, and presently has over 1,000 entries containing more than 1,600 models. We describe here the overall organization and procedures of SASBDB paying most attention to user‐relevant information during submission. Perspectives of further developments, in particular, with OneDep system of the Protein Data Bank, and also widening of SASBDB including new types of data/models are discussed.     

Session-to-session variations in external load measures during small-sided games in professional soccer players

The aims of this study were 1) to analyse session-to-session variations in different external load measures and 2) to examine differences in within-session intervals across different small-sided game (SSG) formats in professional players. Twenty professional soccer players (mean ± SD; age 28.1 ± 4.6 years, height 176.7 ± 4.9 cm, body mass 72.0 ± 7.8 kg, and body fat 10.3 ± 3.8%) participated in 3v3, 4v4, and 6v6 SSGs under different conditions (i.e., touch limitations and presence of goalkeepers vs. free touch and ball possession drill) over three sessions. Selected external load measures—including total distance (TD), high-intensity running (HIR, distance covered > 14.4 km^.h^-1), high-speed running (HSR, distance covered > 19.8 km^.h^-1), and mechanical work (MW, accelerations and deceleration > 2.2 m^.s²)—were recorded using GPS technology during all SSG sessions. Small to large standardized typical errors were observed in session-to-session variations of selected measures across SSGs. TD^.min^-1 showed less variability, having a coefficient of variation (CV) of 2.2 to 4.6%, while all other selected external load measures had CV values ranging from 7.2% to 29.4%. Trivial differences were observed between intervals in TD^.min^-1 and HIR^.min^-1 for all SSGs, as well as in HSR^.min^-1 and MW^.min^-1 for most SSG formats. No reductions or incremental trends in session-to-session variations were observed when employing touch limitations or adding goalkeepers. The increased noise observed in higher speed zones (e.g., high-speed running) suggests a need for more controlled, running-based conditional drills if the aim is greater consistency in these measures.     

A systematic review of collective tactical behaviour in futsal using positional data

Although many studies on collective tactical behaviour have been published in the last decade, no study has revised and summarized the findings provided for futsal. The main aim of this systematic review was to identify and discuss the geometrical centre (GC), distance and area tactical variables used to assess team behaviour in futsal. In addition, it summarizes the findings on the tactical response during futsal competition and training. A systematic review of the relevant articles provided on futsal was carried out using seven electronic databases (SPORTDiscus, ProQuest, Cochrane Plus, Scopus, Google Scholar, PubMed and Web of Science) until September 25, 2019. From a total of 1,209 studies initially found, 12 were included in the qualitative synthesis. There were some trends in the analysis of positional data in futsal with the most relevant situations analysed being 1 vs 1 and 5 vs 4+Goalkeeper. The distances and angles between two points were the most assessed tactical variables. Five types of distance variables were used to assess collective tactical behaviour in futsal: GC-GC, GC-player, player-player, player-ball and player-space. Pressure (GC-GC) was greater in shots on goal than in tackles during professional futsal matches. Area variables were reduced to occupied space, exploration space and dominant area. Occupied space was measured only during competition while the dominant area was measured only during training sessions. The surface area and dominant regions were greater when players were attacking in comparison to when they were defending. In addition, two non-linear techniques (i.e. relative phase and entropy) were applied to analyse synchronisation and complexity and regularity or predictability. Defenders were highly synchronous, while attackers tried to break this coordination to achieve possibilities for action. Task constraints are suitable to induce different regularity patterns. This review is an opportunity to develop studies aimed at bridging the gap in collective tactical behaviour in futsal.     

Reconsidering anion inhibitors in the general context of drug design studies of modulators of activity of the classical enzyme carbonic anhydrase

Inorganic anions inhibit the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1) generally by coordinating to the active site metal ion. Cyanate was reported as a non-coordinating CA inhibitor but those erroneous results were subsequently corrected by another group. We review the anion CA inhibitors (CAIs) in the more general context of drug design studies and the discovery of a large number of inhibitor classes and inhibition mechanisms, including zinc binders (sulphonamides and isosteres, dithiocabamates and isosteres, thiols, selenols, benzoxaboroles, ninhydrins, etc.); inhibitors anchoring to the zinc-coordinated water molecule (phenols, polyamines, sulfocoumarins, thioxocoumarins, catechols); CAIs occluding the entrance to the active site (coumarins and derivatives, lacosamide), as well as compounds that bind outside the active site. All these new chemotypes integrated with a general procedure for obtaining isoform-selective compounds (the tail approach) has resulted, through the guidance of rigorous X-ray crystallography experiments, in the development of highly selective CAIs for all human CA isoforms with many pharmacological applications.     

Unconstrained evolution in short introns? – An analysis of genome‐wide polymorphism and divergence data from Drosophila

An unconstrained reference sequence facilitates the detection of selection. In Drosophila, sequence variation in short introns seems to be least influenced by selection and dominated by mutation and drift. Here, we test this with genome‐wide sequences using an African population (Malawi) of D. melanogaster and data from the related outgroup species D. simulans, D. sechellia, D. erecta and D. yakuba. The distribution of mutations deviates from equilibrium, and the content of A and T (AT) nucleotides shows an excess of variance among introns. We explain this by a complex mutational pattern: a shift in mutational bias towards AT, leading to a slight nonequilibrium in base composition and context‐dependent mutation rates, with G or C (GC) sites mutating most frequently in AT‐rich introns. By comparing the corresponding allele frequency spectra of AT‐rich vs. GC‐rich introns, we can rule out the influence of directional selection or biased gene conversion on the mutational pattern. Compared with neutral equilibrium expectations, polymorphism spectra show an excess of low frequency and a paucity of intermediate frequency variants, irrespective of the direction of mutation. Combining the information from different outgroups with the polymorphism data and using a generalized linear model, we find evidence for shared ancestral polymorphism between D. melanogaster and D. simulans, D. sechellia, arguing against a bottleneck in D. melanogaster. Generally, we find that short introns can be used as a neutral reference on a genome‐wide level, if the spatially and temporally varying mutational pattern is accounted for.     

Low concentrations of isothiocyanates protect mesenchymal stem cells from oxidative injuries, while high concentrations exacerbate DNA damage

Isothiocyanates (ITCs) are molecules naturally present in many cruciferous vegetables (broccoli, black radish, daikon radish, and cauliflowers). Several studies suggest that cruciferous vegetable consumption may reduce cancer risk and slow the aging process. To investigate the effect of ITCs on cellular DNA damage, we evaluated the effects of two different ITCs [sulforaphane (SFN) and raphasatin (RPS)] on the biology of human mesenchymal stem cells (MSCs), which, in addition to their ability to differentiate into mesenchymal tissues, contribute to the homeostatic maintenance of many organs. The choice of SFN and RPS relies on two considerations: they are among the most popular cruciferous vegetables in the diet of western and eastern countries, respectively, and their bioactive properties may differ since they possess specific molecular moiety. Our investigation evidenced that MSCs incubated with low doses of SFN and RPS show reduced in vitro oxidative stress. Moreover, these cells are protected from oxidative damages induced by hydrogen peroxide, while no protection was evident following treatment with the UV ray of a double strand DNA damaging drug, such as doxorubicin. High concentrations of both ITCs induced cytotoxic effects in MSC cultures and further increased DNA damage induced by peroxides. In summary, our study suggests that ITCs, at low doses, may contribute to slowing the aging process related to oxidative DNA damage. Moreover, in cancer treatment, low doses of ITCs may be used as an adjuvant to reduce chemotherapy-induced oxidative stress, while high doses may synergize with anticancer drugs to promote cell DNA damage.     

Hyperproliferation of mitotically active germ cells due to defective anti-Müllerian hormone signaling mediates sex reversal in medaka

The function of AMH (Anti-Müllerian hormone), a phylogenetically ancient member of the TGFβ family of proteins, in lower vertebrates is largely unknown. Previously, we have shown that the gene encoding the type II anti-Müllerian hormone receptor, amhrII, is responsible for excessive germ cell proliferation and male-to-female sex reversal in the medaka hotei mutant. In this study, functional analyses in cultured cells and of other amhrII mutant alleles indicate that lack of AMH signaling causes the hotei phenotype. BrdU incorporation experiments identified the existence of both quiescent and mitotically active germ cells among the self-renewing, type I population of germ cells in the developing gonad. AMH signaling acts in supporting cells to promote the proliferation of mitotically active germ cells but does not trigger quiescent germ cells to proliferate in the developing gonad. Furthermore, we show that the male-to-female sex reversal phenotype in hotei mutants is not a direct consequence of AMH signaling in supporting cells, but is instead mediated by germ cells. Our data demonstrate that interfollicular AMH signaling regulates proliferation at a specific stage of germ cell development, and that this regulation is crucial for the proper manifestation of gonadal sex directed by sex determination genes.     

Thiol synthetases of legumes: immunogold localization and differential gene regulation by phytohormones

In plants and other organisms, glutathione (GSH) biosynthesis is catalysed sequentially by γ-glutamylcysteine synthetase (γECS) and glutathione synthetase (GSHS). In legumes, homoglutathione (hGSH) can replace GSH and is synthesized by γECS and a specific homoglutathione synthetase (hGSHS). The subcellular localization of the enzymes was examined by electron microscopy in several legumes and gene expression was analysed in Lotus japonicus plants treated for 1-48 h with 50 μM of hormones. Immunogold localization studies revealed that γECS is confined to chloroplasts and plastids, whereas hGSHS is also in the cytosol. Addition of hormones caused differential expression of thiol synthetases in roots. After 24-48 h, abscisic and salicylic acids downregulated GSHS whereas jasmonic acid upregulated it. Cytokinins and polyamines activated GSHS but not γECS or hGSHS. Jasmonic acid elicited a coordinated response of the three genes and auxin induced both hGSHS expression and activity. Results show that the thiol biosynthetic pathway is compartmentalized in legumes. Moreover, the similar response profiles of the GSH and hGSH contents in roots of non-nodulated and nodulated plants to the various hormonal treatments indicate that thiol homeostasis is independent of the nitrogen source of the plants. The differential regulation of the three mRNA levels, hGSHS activity, and thiol contents by hormones indicates a fine control of thiol biosynthesis at multiple levels and strongly suggests that GSH and hGSH play distinct roles in plant development and stress responses.     

Anion inhibition studies of the fastest carbonic anhydrase (CA) known,the extremo-CA from the bacterium Sulfurihydrogenibium azorense

The α-carbonic anhydrase (CA, EC 4.2.1.1) from the extremophilic bacterium Sulfurihydrogenibium azorense, SazCA, is the fastest CA known to date as a catalyst for CO₂ hydration to bicarbonate and protons. We report an inhibition study of this enzyme with inorganic anions and several other small molecules known to interact with these metalloenzymes. Bicarbonate, carbonate and sulfate were ineffective SazCA inhibitors whereas most other inorganic anions were submillimolar inhibitors. The best inhibition was observed with trithiocarbonate, diethyldithiocarbamate, sulfamide, sulfamate, phenylboronic, and phenylarsonic acid, which showed inhibition constants in the range of 3–39 μM. As SazCA is very stable at high temperatures (being an ‘extremo-CA’) and very effective as a catalyst, the inhibition studies reported here may be crucial for designing biotechnological applications for this enzyme, for example for CO₂ capture processes.