Fast and automated functional classification with MED‐SuMo: An application on purine‐binding proteins

Ligand–protein interactions are essential for biological processes, and precise characterization of protein binding sites is crucial to understand protein functions. MED‐SuMo is a powerful technology to localize similar local regions on protein surfaces. Its heuristic is based on a 3D representation of macromolecules using specific surface chemical features associating chemical characteristics with geometrical properties. MED‐SMA is an automated and fast method to classify binding sites. It is based on MED‐SuMo technology, which builds a similarity graph, and it uses the Markov Clustering algorithm. Purine binding sites are well studied as drug targets. Here, purine binding sites of the Protein DataBank (PDB) are classified. Proteins potentially inhibited or activated through the same mechanism are gathered. Results are analyzed according to PROSITE annotations and to carefully refined functional annotations extracted from the PDB. As expected, binding sites associated with related mechanisms are gathered, for example, the Small GTPases. Nevertheless, protein kinases from different Kinome families are also found together, for example, Aurora‐A and CDK2 proteins which are inhibited by the same drugs. Representative examples of different clusters are presented. The effectiveness of the MED‐SMA approach is demonstrated as it gathers binding sites of proteins with similar structure‐activity relationships. Moreover, an efficient new protocol associates structures absent of cocrystallized ligands to the purine clusters enabling those structures to be associated with a specific binding mechanism. Applications of this classification by binding mode similarity include target‐based drug design and prediction of cross‐reactivity and therefore potential toxic side effects.     

Label-free and amplified quantitation of proteins in complex mixtures using diffractive optics technology

Immunoaffinity approaches remain invaluable tools for characterization and quantitation of biopolymers. Their application in separation science is often limited due to the challenges of immunoassay development. Typical end-point immunoassays require time consuming and labor-intensive approaches for optimization. Real-time label-free analysis using diffractive optics technology (dot^®) helps guide a very effective iterative process for rapid immunoassay development. Both label-free and amplified approaches can be used throughout feasibility testing and ultimately in the final assay, providing a robust platform for biopolymer analysis over a very broad dynamic range. We demonstrate the use of dot in rapidly developing assays for quantitating (1) human IgG in complex media, (2) a fusion protein in production media and (3) protein A contamination in purified immunoglobulin preparations.     

GC/MS based identification of skunk spray maliciously deployed as “biological weapon” to harm civilians

Our laboratory has been asked to elucidate the origin of a strong “toxic smell” present in a prominent politician's office, private house and motorcar. This stinky and pungent atmosphere has caused serious nausea and vomiting to several individuals. Urine samples were collected from the persons presenting symptoms of nausea for toxicological analysis. Drops, paper and cotton swabs of an oily liquid found at the implicated places were submitted by police to our laboratory for investigation. Methanol extracts of the drops were acetylated for gas chromatography/mass spectrometry (GC/MS) analysis in the electron impact mode; the cotton and paper swabs were analysed using headspace-gas chromatography/mass spectrometry (HS-GC/MS). The GC/MS analysis of the acetylated methanol extracts revealed that the major peaks of the chromatogram could be attributed to 2-methylquinoline, to 2-quinolinemethanethiol, to S-2-quinolinemethyl thioacetate, to 2-phenylethanethiol, to bis(E)-2-butenyl disulphide and to bis(3-methylbutyl) disulphide. Several volatile sulphur-containing compounds have been identified with the HS-GC/MS system. Detailed examination of the spectra as well as GC/MS analysis of commercially available skunk secret allowed us to relate the identified compounds to those present in the defence spray of skunks. No health sequels were observed for any of the persons implicated in this case.     

Acute metal stress in Populus tremula×P. alba (717‐1B4 genotype): Leaf and cambial proteome changes induced by cadmium2+

The comprehension of metal homeostasis in plants requires the identification of molecular markers linked to stress tolerance. Proteomic changes in leaves and cambial zone of Populus tremula×P. alba (717‐1B4 genotype) were analyzed after 61 days of exposure to cadmium (Cd) 360 mg/kg soil dry weight in pot‐soil cultures. The treatment led to an acute Cd stress with a reduction of growth and photosynthesis. Cd stress induced changes in the display of 120 spots for leaf tissue and 153 spots for the cambial zone. It involved a reduced photosynthesis, resulting in a profound reorganisation of carbon and carbohydrate metabolisms in both tissues. Cambial cells underwent stress from the Cd actually present inside the tissue but also a deprivation of photosynthates caused by leaf stress. An important tissue specificity of the response was observed, according to the differences in cell structures and functions.     

New species of <Emphasis Type="Italic">Pleonotoma</Emphasis> (Bignonieae,Bignoniaceae) from Amazonia,Brazil

Two new species of Pleonotoma Miers (Bignonieae, Bignoniaceae) from Brazilian Amazonia are described and illustrated: Pleonotoma fissicalyx B. M. Gomes & Proen?a and P. longiflora B. M. Gomes & Proen?a. P. fissicalyx is characterised by foliaceous prophylls of the axillary bud, 3-ternate leaves, a large number of short racemes concentrated at the apex of the flowering branch with many visible pedicel scars, a laterally fissured, almost spathaceous calyx, and a small, narrow hypocrateriform corolla with subexserted anthers; the fruits are unknown. P. longiflora is characterised by the combination of weakly tetragonal branchlets with unribbed angles, non-foliaceous, flat, rounded prophylls of axillary bud with an eccentric tip, 2-ternate leaves, broad axillary racemes, an elongate tubular calyx and a hypocrateriform corolla up to 12 cm long; its inclusion within Pleonotoma is confirmed by molecular phylogeny.     

Comparative analysis of nonaspanin protein sequences and expression studies in zebrafish

Nonaspanins constitute a family of proteins, also called TM9SF, characterized by a large non-cytoplasmic domain and nine putative transmembrane domains. This family is highly conserved through evolution and comprises three members in Saccharomyces cerevisiae, Dictyostelium discoideum, and Drosophila melanogaster, and four members are reported in mammals (TM9SF1–TM9SF4). Genetic studies in Dictyostelium and Drosophila have shown that TM9SF members are required for adhesion and phagocytosis in innate immune response, furthermore, human TM9SF1 plays a role in the regulation of autophagy and human TM9SF4 in tumor cannibalism. Here we report that the zebrafish genome encodes five members of this family, TM9SF1–TM9SF5, which show high level of sequence conservation with the previously reported members. Expression analysis in zebrafish showed that all members are maternally expressed and continue to be present throughout embryogenesis to adults. Gene expression could not be regulated by pathogen-associated molecular patterns such as LPS, CpG, or Poly I:C. By bioinformatic analyses of 80 TM9SF protein sequences from yeast, plants, and animals, we confirmed a very conserved protein structure. An evolutionary conserved immunoreceptor tyrosine-based inhibition motif has been detected in the cytoplasmic domain between transmembrane domain (TM) 7 and TM8 in TM9SF1, TM9SF2, TM9SF4 and TM9SF5, and at the extreme C-terminal end of TM9SF4. Finally, a conserved TRAF2 binding domain could also be predicted in the cytoplasmic regions of TM9SF2, TM9SF3, TM9SF4, and TM9SF5. This confirms the hypothesis that TM9SF proteins may play a regulatory role in a specific and ancient cellular mechanism that is involved in innate immunity.     

Desiccation tolerance in <Emphasis Type="Italic">Pleurostima purpurea</Emphasis> (Velloziaceae)

Previous works suggested that Pleurostima purpurea (Velloziaceae—Barbacenioideae) shows a remarkable capacity to endure desiccation of its vegetative tissues. P. purpurea occurs in monocotyledons mats on soil islands in the Pão de Açucar (Sugar Loaf) one of the most recognizable rock outcrops of the world, in Rio de Janeiro, southeastern Brazil. Mats of P. purpurea occur in cliffs by the sea some meters above the tidal zone. Although living in rock outcrops almost devoid of any soil cover, P. purpurea seems to occur preferably on less exposed rock faces and slightly shady sites. Usually, less extreme adaptations to drought would be expected in plants with the habitat preference of P. purpurea. Relying on this observation, we argue if a combination of different strategies of dealing with low water availability can be found in P. purpurea as on other desiccation tolerant angiosperms. This study aims to examine the occurrence of desiccation tolerant behavior in P. purpurea together with the expression of drought avoidance mechanisms during dehydration progression. For this, it was analyzed the gas exchanges, leaf pigments and relative leaf water content during desiccation and rehydration of cultivated mature individuals. P. purpurea behaved like typical drought avoiders under moderated drought condition with stomatal closure occurring around a relative leaf water content up to 90%. During this process, it was observed a delay in the leaf relative water content (RWC _leaf) decrease comparing to the plant-soil relative water content (RWC _plant-soil). As soil dehydration worsened, gas exchanges restrictions progressed until a lack of activity which characterizes anabiosis. The loss of chlorophyll occurs before the end of total dehydration, characterizing the presence of poikilochlorophylly. The chlorophyll degradation follows the RWC _leaf decrease, which achieved the minimum average value of 17% without incurring in leaf abscission. The chlorophyll re-synthesis seems to start well after the full rehydration of the leaf. During all of this process, carotenoid content remained stable. These results are coherent with a combination of drought avoidance and desiccation tolerance in P. purpurea which seems to be coherent with the amplitude of water availability in the rock outcrop habitat where it occurs, suggesting that the periods of water availability are sufficiently long for the success of the costly desiccation tolerant behavior but too short to make a typical drought avoider species win the competition for exploring the rock outcrop substrate where P. purpurea occurs.     

Is caseinomacropeptide from milk proteins,an inhibitor of gastric secretion?

The aim of this work was to study, in vivo, the effect of the ingestion of not glycosylated caseinomacropeptide (CMP) on gastric secretion. In Experiments #1 and #2, 7 calves fitted with a gastric pouch received either a diet without CMP (C diet) or C diet in which CMP was introduced (equal to and 5 folds that of CMP quantity contained in cow milk, diets CMP1 and CMP5, respectively). In Experiment #3, 2 calves (with gastric pouch) were fed C diet followed by an “iv perfusion” of CMP. In Experiment #4, 25 calves fed either C, CMP1 or CMP5 diets were fitted with a blood catheter for sample collections. The quantities of daily gastric secretions seemed few modified by CMP ingestion but the profile of these secretions was changed along the day. The most important result is that CMP can inhibit gastric secretions (mainly hydrochloric acid) stimulated by the meal, but there was no dose-dependent response. No similar observations were obtained after perfusion of CMP in jugular vein. CMP was not detected in blood. Results obtained in our experiments are not in favor of its significant intestinal absorption. Gastrin, somatostatin and VIP could be implicated in the mechanisms of regulation.     

Effect of Artichoke Leaf Extract on Hepatic and Cardiac Oxidative Stress in Rats Fed on High Cholesterol Diet

Hypercholesterolemia and lipid peroxidation play complementary roles in atherosclerosis. Artichoke (Cynara scolymus L., Asteraceae) leaf extract (ALE), rich in antioxidants, has cholesterol-reducing effect. We investigated the effect of ALE on serum and hepatic lipid levels and pro-oxidant–antioxidant balance in the liver and heart of hypercholesterolemic rats. Rats were fed on 4% (w/w) cholesterol and 1% cholic acid (w/w) supplemented diet for 1 month. ALE (1.5 g/kg/day) was given by gavage during the last 2 weeks. High cholesterol (HC) diet caused significant increases in serum and liver cholesterol and triglyceride levels. It increased malondialdehyde (MDA) and diene conjugate (DC) levels in both tissues. Hepatic vitamin E levels and hepatic and cardiac glutathione peroxidase (GSH-Px) activities decreased, but superoxide dismutase and glutathione transferase activities, glutathione, and vitamin C levels remained unchanged due to HC diet. Serum cholesterol and triglyceride levels and ratio of cholesterol to high-density lipoprotein (HDL)-cholesterol decreased in ALE plus HC-treated rats, but liver cholesterol and triglyceride levels remained unchanged. Significant decreases in hepatic and cardiac MDA and DC levels and increases in hepatic vitamin E and GSH-Px activities were observed in ALE-treated hypercholesterolemic rats. Our results indicate that ALE decreases serum lipids and hypercholesterolemia-induced pro-oxidant state in both tissues.