Biological influences on inter- and intraspecific isotopic variability among paired chondrostome fishes

This study aimed at examining resource partitioning both at the inter- and intraspecific levels between paired chondrostome fishes: Chondrostoma nasus, the nase, C. toxostoma, the sofie, and their hybrid. The study was performed in the south of France and concerned a main river (the Durance River) and a tributary (the Buech River). In these rivers, C. nasus was an introduced species, originating in central Europe, and C. toxostoma was an endemic congener, in the south of France. Stable isotope analysis was used to analyse trophic and spatial niches. Isotopic differences indicated that individuals from the three taxa (C. nasus, C. toxostoma and their hybrid) have different spatial origins. At the interspecific level, the different chondrostomes originating from the Buech River showed a high level of trophic niche overlap. At the intraspecific level, nase individuals originating from the different spatial origins showed a resource polymorphism; differences in morphology were associated with variation in behaviour and life history traits. Their coexistence was a likely outcome of resource polymorphism. This study provides an example of the importance of considering the link between intra- and interspecific interactions to gain an understanding of the mechanisms driving the coexistence of species-pairs.     

Assessment of the immunomodulatory activity of cheese extracts by a complete and easy to handle <Emphasis Type="Italic">in</Emphasis><Emphasis Type="Italic">vitro</Emphasis> screening methodology

A simple and rapid screening methodology based on the in vitro culture of murine hybridoma and human T-lymphocytes was developed to assess the potential immunomodulatory activity of water-soluble extracts (WSE) from cheese. The two immune cell lines were cultured in microplates with or without cheese WSE. The proliferation and the metabolic activity of cells were monitored at their different growth phases by the BrdU (5-bromo-2′-deoxyuridine) and MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenylterazolium bromide] assays, respectively. WSE from Abondance cheese enhanced DNA synthesis and the metabolic activity of the hybridoma cells (1.2-and 1.3-to 1.6-fold of the control, respectively) and also of the T lymphocytes (1.5-fold of the control) for almost all of the dilutions tested. To evaluate the validity of the results obtained following this screening methodology, hybridoma and T-lymphocyte cells were cultivated in 50 ml flasks: the maximal cell density was increased by about 10–16% in presence of cheese WSE for both cell lines and the antibody production by the hybridoma cells was increased by 50%.     

Urinary marker of oral pregnenolone administration

Pregnenolone (PREG) can potentially be abused by athletes to maintain an equilibration of the steroidal environment after sex steroids administrations. Five men volunteers orally ingested 50 mg PREG to determine optimal urinary markers for detection of this steroid. Our findings show that ingestion of PREG has no significant effects on the testosterone/epitestosterone (T/E) and testosterone/luteinizing hormone (T/LH) ratios, whereas variable changes on the carbon isotopic values of three T metabolites: androsterone, etiocholanolone, 5beta-androstane-3alpha,17beta-diol (5beta-androstanediol) together with 16(5alpha)-androsten-3alpha-ol (androstenol) and 5beta-pregnane-3alpha,20alpha-diol (pregnanediol) have been observed. The difference between the carbon isotopic values (delta13C-values) of androstenol and pregnanediol is potentially the most reliable marker of exogenous PREG administration in males. For all subjects, the differences differ by 3.0 per thousand or more over a period of about 10 h and for both of them the detection window for positivity is extended over 40 h.     

Estrogens Induce Rapid Cytoskeleton Re-Organization in Human Dermal Fibroblasts via the Non-Classical Receptor GPR30

The post-menopausal decrease in estrogen circulating levels results in rapid skin deterioration pointing out to a protective effect exerted by these hormones. The identity of the skin cell type responding to estrogens is unclear as are the cellular and molecular processes they elicit. Here, we reported that lack of estrogens induces rapid re-organization of the human dermal fibroblast cytoskeleton resulting in striking cell shape change. This morphological change was accompanied by a spatial re-organization of focal adhesion and a substantial reduction of their number as evidenced by vinculin and actin co-staining. Cell morphology and cytoskeleton organization was fully restored upon 17β-estradiol (E2) addition. Treatment with specific ER antagonists and cycloheximide respectively showed that the E2 acts independently of the classical Estrogen Receptors and that cell shape change is mediated by non-genomic mechanisms. E2 treatment resulted in a rapid and transient activation of ERK1/2 but not Src or PI3K. We show that human fibroblasts express the non-classical E2 receptor GPR30 and that its agonist G-1 phenocopies the effect of E2. Inhibiting GPR30 through treatment with the G-15 antagonist or specific shRNA impaired E2 effects. Altogether, our data reveal a novel mechanism by which estrogens act on skin fibroblast by regulating cell shape through the non-classical G protein-coupled receptor GPR30 and ERK1/2 activation.     

Habitat Selectivity and Reliance on Live Corals for Indo-Pacific Hawkfishes (Family: Cirrhitidae)

Hawkfishes (family: Cirrhitidae) are small conspicuous reef predators that commonly perch on, or shelter within, the branches of coral colonies. This study examined habitat associations of hawkfishes, and explicitly tested whether hawkfishes associate with specific types of live coral. Live coral use and habitat selectivity of hawkfishes was explored at six locations from Chagos in the central Indian Ocean extending east to Fiji in the Pacific Ocean. A total of 529 hawkfishes from seven species were recorded across all locations with 63% of individuals observed perching on, or sheltering within, live coral colonies. Five species (all except Cirrhitus pinnulatus and Cirrhitichthys oxycephalus) associated with live coral habitats. Cirrhitichthys falco selected for species of Pocillopora while Paracirrhites arcatus and P. forsteri selected for both Pocillopora and Acropora, revealing that these habitats are used disproportionately more than expected based on the local cover of these coral genera. Habitat selection was consistent across geographic locations, and species of Pocillopora were the most frequently used and most consistently selected even though this coral genus never comprised more than 6% of the total coral cover at any of the locations. Across locations, Paracirrhites arcatus and P. forsteri were the most abundant species and variation in their abundance corresponded with local patterns of live coral cover and abundance of Pocilloporid corals, respectively. These findings demonstrate the link between small predatory fishes and live coral habitats adding to the growing body of literature highlighting that live corals (especially erect branching corals) are critically important for sustaining high abundance and diversity of fishes on coral reefs.     

Synthesis of an Enantiomerically Pure Carbocyclic DNA Abasic Site Analogue

Abstract

A short synthetic route to an appropriately derivatized carbocyclic analogue of abasic site residues of DNA is proposed.     

Nepenthesin from Monkey Cups for Hydrogen/Deuterium Exchange Mass Spectrometry

Studies of protein dynamics, structure and interactions using hydrogen/deuterium exchange mass spectrometry (HDX-MS) have sharply increased over the past 5–10 years. The predominant technology requires fast digestion at pH 2–3 to retain deuterium label. Pepsin is used almost exclusively, but it provides relatively low efficiency under the constraints of the experiment, and a selectivity profile that renders poor coverage of intrinsically disordered regions. In this study we present nepenthesin-containing secretions of the pitcher plant Nepenthes, commonly called monkey cups, for use in HDX-MS. We show that nepenthesin is at least 1400-fold more efficient than pepsin under HDX-competent conditions, with a selectivity profile that mimics pepsin in part, but also includes efficient cleavage C-terminal to “forbidden” residues K, R, H, and P. High efficiency permits a solution-based analysis with no detectable autolysis, avoiding the complication of immobilized enzyme reactors. Relaxed selectivity promotes high coverage of disordered regions and the ability to “tune” the mass map for regions of interest. Nepenthesin-enriched secretions were applied to an analysis of protein complexes in the nonhomologous end-joining DNA repair pathway. The analysis of XRCC4 binding to the BRCT domains of Ligase IV points to secondary interactions between the disordered C-terminal tail of XRCC4 and remote regions of the BRCT domains, which could only be identified with a nepenthesin-based workflow. HDX data suggest that stalk-binding to XRCC4 primes a BRCT conformation in these remote regions to support tail interaction, an event which may be phosphoregulated. We conclude that nepenthesin is an effective alternative to pepsin for all HDX-MS applications, and especially for the analysis of structural transitions among intrinsically disordered proteins and their binding partners.Mass spectrometry has served the biochemical and biological communities by providing the capacity for protein identification and characterization, but in the last several years it has also become a powerful tool for interrogating protein structure and dynamics (1, 2). Solution-phase hydrogen/deuterium exchange (HDX)¹, when coupled with mass spectrometry (MS), provides rich sets of data that can be mined to extract structural and dynamic parameters from proteins (3–7). In many cases, the technique is used in experimental situations in which x-ray diffraction analysis or other biophysical techniques (e.g. NMR, cryoEM) are difficult to apply, which is particularly true in the structure-function analysis of protein interactions (8). Most applications of the method involve deuteration of a protein in two or more states, and differential labeling data is extracted at the highest structural resolution possible. Although there have been some impressive developments in top-down protein analysis using newer ion fragmentation methods for label localization (9, 10), most studies continue to employ a bottom-up strategy, in which the protein is digested with an enzyme, and the label is quantified by mass analysis of the resulting peptides.The reasons for the prominence of the bottom-up approach to HDX-MS are shared with the corresponding proteomics method. Peptides may be detected with more sensitivity than proteins, and samples of considerably higher complexity can be interrogated (11). Analytically, this shifts the focus toward optimizing protein digestion, to cover 100% of the sequence and generate a high degree of overlapping fragments to increase opportunities for localizing the deuterium label at high resolution (12–14).The unique requirements of the HDX-MS workflow unfortunately place restrictions on the digestion enzymes that may be used. To avoid label loss through back-exchange to nondeuterated solvent, the kinetics of exchange must be dramatically slowed by pH and temperature reduction, and even under these conditions the digestion must be done rapidly. Conventional methods employ a pH of ∼2.5 and temperatures of 4–10 °C. The aspartic protease pepsin can function under such conditions, which has led to its prominence for HDX-MS applications. This does not mean the enzyme is ideal. Several laboratories have sought to identify other enzymes or develop analytical solutions that address its shortcomings, which include extensive autolysis, modest efficiency, and nonideal substrate specificity. Currently, most methods involve either enzyme microreactors presenting high concentrations of pepsin in a flow-through system (15), or solution-phase digestions using pepsin and protease XIII in separate experiments (16, 17). The latter enzyme is also an aspartic protease with a sequence specificity that partially overlaps pepsin, thus the two maps together tend to somewhat improve sequence coverage (18). A method that fuses the two strategies has recently been described, involving tandem pepsin and protease XIII microreactors (13).Neither strategy is likely to be ideal when applied to protein complexes of far greater complexity, to support of structure-building activities or dynamics analysis of multiprotein “machines.” The microreactor approach complicates the front-end fluidic system, and can lead to sample loss and carryover (19). The solution-phase method requires large amounts of enzyme resulting in contamination because of enzyme autolysis (18). More importantly, neither fully overcomes the low efficiency of these enzymes. In many cases, changing the presentation of substrate can change the sequence map considerably. For example, the sequence map of a protein can be distorted when bound to a second protein (20). A map dependent on the protein load complicates the comparison of deuteration levels for the protein in different states. This alteration suggests a level of substrate inhibition (21), and probably reflects a wide range of specificity constants (k_cat/K_m) across the many individual cleavage sites presented in a protein substrate (22). Similar issues have been noted with trypsin (23). Overall, the sequence maps generated using these methods are serviceable for samples of lower complexity, but low enzymatic efficiency of the available proteases remains an important limitation and a key driver in the search for novel proteases (24).In this study, we characterize the proteolytic activity of secretions from the Nepenthes genus (25), arising from the aspartic protease nepenthesin (26), and evaluate the enzyme for use within HDX applications. Nepenthesin displays remarkably high cleavage efficiency for a broad range of substrates at low pH and temperature, which promotes high sequence coverage for a collection of proteins selected from ongoing HDX projects in our laboratories. Globally, we demonstrate that it outperforms pepsin in sequence coverage and can be used in a simple workflow for broad sequence coverage, or targeted toward a desired area of protein sequence. This new tool was applied to an HDX-MS characterization of a protein complex involved in the nonhomologous end-joining (NHEJ) pathway of DNA damage repair, and the results support a model of the complex proposed from SAXS data (27).