An FPGA implementation to detect selective cationic antibacterial peptides

Exhaustive prediction of physicochemical properties of peptide sequences is used in different areas of biological research. One example is the identification of selective cationic antibacterial peptides (SCAPs), which may be used in the treatment of different diseases. Due to the discrete nature of peptide sequences, the physicochemical properties calculation is considered a high-performance computing problem. A competitive solution for this class of problems is to embed algorithms into dedicated hardware. In the present work we present the adaptation, design and implementation of an algorithm for SCAPs prediction into a Field Programmable Gate Array (FPGA) platform. Four physicochemical properties codes useful in the identification of peptide sequences with potential selective antibacterial activity were implemented into an FPGA board. The speed-up gained in a single-copy implementation was up to 108 times compared with a single Intel processor cycle for cycle. The inherent scalability of our design allows for replication of this code into multiple FPGA cards and consequently improvements in speed are possible. Our results show the first embedded SCAPs prediction solution described and constitutes the grounds to efficiently perform the exhaustive analysis of the sequence-physicochemical properties relationship of peptides.     

Behavioural response thresholds in New Zealand crab megalopae to ambient underwater sound

A small number of studies have demonstrated that settlement stage decapod crustaceans are able to detect and exhibit swimming, settlement and metamorphosis responses to ambient underwater sound emanating from coastal reefs. However, the intensity of the acoustic cue required to initiate the settlement and metamorphosis response, and therefore the potential range over which this acoustic cue may operate, is not known. The current study determined the behavioural response thresholds of four species of New Zealand brachyuran crab megalopae by exposing them to different intensity levels of broadcast reef sound recorded from their preferred settlement habitat and from an unfavourable settlement habitat. Megalopae of the rocky-reef crab, Leptograpsus variegatus, exhibited the lowest behavioural response threshold (highest sensitivity), with a significant reduction in time to metamorphosis (TTM) when exposed to underwater reef sound with an intensity of 90 dB re 1 μPa and greater (100, 126 and 135 dB re 1 μPa). Megalopae of the mud crab, Austrohelice crassa, which settle in soft sediment habitats, exhibited no response to any of the underwater reef sound levels. All reef associated species exposed to sound levels from an unfavourable settlement habitat showed no significant change in TTM, even at intensities that were similar to their preferred reef sound for which reductions in TTM were observed. These results indicated that megalopae were able to discern and respond selectively to habitat-specific acoustic cues. The settlement and metamorphosis behavioural response thresholds to levels of underwater reef sound determined in the current study of four species of crabs, enables preliminary estimation of the spatial range at which an acoustic settlement cue may be operating, from 5 m to 40 km depending on the species. Overall, these results indicate that underwater sound is likely to play a major role in influencing the spatial patterns of settlement of coastal crab species.     

L'ultrastruttura dell'organo dell'emolinfa nella larva di Drosophila melanogaster

Summary The structures formerly described as blood-forming organs or lymph glands in Drosophila melanogaster were re-examined by means of phase contrast, polarized light, and electron microscopy. As a result, the term haemolymph organ is suggested as more appropriate for these peculiar organs. Haemolymph organs of second and third instar larvae, and first stage (white) pupae from a wild strain (Varese) were studied; the methods are described in detail.The haemolymph organ consists of two voluminous anterior lobes and several smaller posterior ones that are ovoid or tubular in shape. The anterior lobes comprise an outer capsule containing some muscle cells, a supporting stroma, and various kinds of cells. The stroma appears to consist of lamellated material of scleroprotein nature similar to that described in other organs of numerous insect species. This material must be considered as a component of the connective tissue characteristic of insect organs.The cells are isolated or organized in groups of various sizes. The following types can be distinguished: rounded cells that are poorly differentiated, polygonal cells with well developed cytoplasm rich in organelles, polygonal cells with clear cytoplasm, and cells that appear to be intermediate form of the types mentioned above.The morphological data presented confirm that the haemolymph organ produces and releases into the haemolymph various types of cells; of these the polygonal cells have a phagocytic and excretory function while only hypotheses can be presented at present concerning the role of the rounded cells. In addition the presence of polygonal cells with clear cytoplasm, showing signs of secretory activity, suggest that the haemolymph organ is involved in the production of substances constituting the fluid fraction of the haemolymph.

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Ricerca eseguita con i sussidi del C.N.R. (Impresa Genetica).     

Application of the yeast Yarrowia lipolytica as a model to analyse human pathogenic mutations in mitochondrial complex I (NADH:ubiquinone oxidoreductase)

While diagnosis and genetic analysis of mitochondrial disorders has made remarkable progress, we still do not understand how given molecular defects are correlated to specific patterns of symptoms and their severity. Towards resolving this dilemma for the largest and therefore most affected respiratory chain enzyme, we have established the yeast Yarrowia lipolytica as a eucaryotic model system to analyse respiratory chain complex I. For in vivo analysis, eYFP protein was attached to the 30-kDa subunit to visualize complex I and mitochondria. Deletions strains for nuclear coded subunits allow the reconstruction of patient alleles by site-directed mutagenesis and plasmid complementation. In most of the pathogenic mutations analysed so far, decreased catalytic activities, elevated K(M) values, and/or elevated I(50) values for quinone-analogous inhibitors were observed, providing plausible clues on the pathogenic process at the molecular level. Leigh mutations in the 49-kDa and PSST homologous subunits are found in regions that are at the boundaries of the ubiquinone-reducing catalytic core. This supports the proposed structural model and at the same time identifies novel domains critical for catalysis. Thus, Y. lipolytica is a useful lower eucaryotic model that will help to understand how pathogenic mutations in complex I interfere with enzyme function.     

Immobilization of enzymes in microtiter plate scale

Different immobilization methods were adapted to the 96-well microtiter plate scale using esterases as model enzymes. The methods tested were based on adsorption, coprecipitation, aggregation and covalent bonding. The protein covered microcrystals proved to be the best method in terms of yield and expressed activity for the test reaction, which was the alcoholysis of p-nitrophenyl acetate with 1-propanol under anhydrous conditions.     

Effect of endurance flight on haematocrit in migrating birds

The effects of an endurance flight on the haematocrit, the percentage of packed red blood cells per blood volume, were examined within the framework of six possible factors explaining possible changes in the haematocrit. Two approaches were adopted: (1) the haematocrit was studied in four species of passerine birds which landed on an Italian island after having crossed the Mediterranean Sea on their spring migration in a non-stop flight; (2) the haematocrit was evaluated in six individual red knots after a flight of 1, 2, 4 and 10 h in a wind tunnel and the data thus obtained compared with data on resting birds with or without food. In the four passerine species, the haematocrit decreased from 51% in fat birds to 48% in lean birds. In lean birds, the haematocrit dropped from 48% in birds with well-developed breast muscles to 36% in birds with emaciated breast muscles. In the red knots, the haematocrit was dependent on body mass in flying and resting birds. The haematocrit decreased from about 51% pre-flight to about 49% within 1 h of flight and remained at this level for up to 10 h of flight. Taking the results from the passerines and the red knots together, it seems that the haematocrit drops by a few percentage points within 1 h after the onset of flight, decreases very slowly with decreasing body mass and decreases more steeply in very lean birds having entered stage III of fasting. This indicates that dehydration is not an underlying factor in decreased haematocrit because if this were the case we would expect an increase with endurance flight. We found no effect of the presence of blood parasites on haematocrit. With the onset of flight, haemodilution may be adaptive, because it reduces blood viscosity and, thereby, energy expenditure by the heart, or it may be a sign of water conservation as an insurance against the risk of dehydration during long non-stop flights. During endurance flight, a reduction in the haematocrit may be adaptive, in that oxygen delivery capacity is adjusted to the decreased oxygen needs as body mass decreases. A decreasing haematocrit would also allow birds to reduce heart beat frequency and/or heart size, because blood viscosity decreases disproportionally with decreasing haematocrit. However, when energy stores are about to come to an end and birds increase protein breakdown, the haematocrit decreases even further, and birds probably become anaemic due to a reduced erythropoiesis.     

Substrate specificity of human kallikrein 6: salt and glycosaminoglycan activation effects

Human kallikrein 6 (hK6) is abundantly expressed in the central nervous system and is implicated in demyelinating disease. This study provided biochemical data about the substrate specificity and activation of hK6 by glycosaminoglycans and by kosmotropic salts, which followed the Hofmeister series. The screening of fluorescence resonance energy transfer (FRET) peptide families derived from Abz-KLRSSKQ-EDDnp resulted in the finding that Abz-AFRFSQ-EDDnp (where Abz is ortho-aminobenzoic acid and EDDnp is N-[2,4-dinitrophenyl]ethylenediamine)) is the best synthetic substrate described so far for hK6 (kcat/Km 38,667 s(-1) mm(-1)). It is noteworthy that the AFRFS sequence was found as a motif in the amino-terminal domain of seven human ionotropic glutamate receptor subunits. We also examined the hK6 hydrolytic activity on FRET peptides derived from human myelin basic protein, precursor of the Abeta amyloid peptide, reactive center loop of alpha1-antichymotrypsin, plasminogen, and maturation and inactivation cleavage sites of hK6, which were described earlier as natural substrates for hK6. The best substrates were derived from myelin basic protein. The hK6 maturation cleavage site was poorly hydrolyzed, and no evidence was found to support a two-step self-activation process reported previously. Finally, we assayed FRET peptides derived from sequences that span the cleavage sites for activation of protease-activated receptors (PAR) 1-4, and only the substrate with the PAR 2 sequence was hydrolyzed. These results further supported the hypothesis that hK6 expressed in the central nervous system is involved in normal myelin turnover/demyelination processes, but it is unlikely to self-activate. This report also suggested the possible modulation of ionotropic glutamate receptors and activation of PAR 2 by hK6.     

Plasma metabolites reflect seasonally changing metabolic processes in a long-distance migrant shorebird (Calidris canutus)

Migrant birds have tightly scheduled annual cycles consisting of several distinct life cycle (sub-)stages such as reproduction, migration, moult and overwintering, each of which have specific metabolic requirements (e.g., fattening during migration, protein build-up during moult). This study examines changes in fat and protein metabolism during the annual cycle of body mass and moult over 1.5 years in a captive flock of an arctic-breeding shorebird, the red knot Calidris canutus islandica. 2-5 h after food withdrawal, plasma uric acid levels were still decreasing and beta-hydroxy-butyrate levels were low, indicating prolonged catabolism of dietary protein, probably linked with a conversion into lipids. Such a late-resorptive state is achieved much earlier in passerines, but only after several days in penguins and, thus, seems to depend on meal size or mass-specific metabolic rate. Substages of body mass gain and high body mass were characterized by increased plasma triglyceride levels reflecting increased turnover of lipids, and low levels of the ketone body beta-hydroxy- butyrate, indicating that the bird is not short of glucose. The high uric acid levels during these substages indicated an increased breakdown of nutritional protein. During moult, plasma triglyceride levels were low, suggesting that lipids were less available than at other times of the year. It is concluded that plasma metabolite levels indicate the metabolic processes related to migratory fuelling and moult and the influence of exogeneous factors.     

The effect of prolyl oligopeptidase inhibition on extracellular acetylcholine and dopamine levels in the rat striatum

Prolyl oligopeptidase (PREP, EC 3.4.21.26) inhibitors have potential as cognition enhancers, but the mechanism of action behind the cognitive effects remains unclear. Since acetylcholine (ACh) and dopamine (DA) are known to be associated with the regulation of cognitive processes, we investigated the effects of two PREP inhibitors on the extracellular levels of ACh and DA in the rat striatum using in vivo microdialysis. KYP-2047 and JTP-4819 were administered either as a single systemic dose (50 μmol/kg～17 mg/kg i.p.) or directly into the striatum by retrodialysis via the microdialysis probe (12.5, 37.5 or 125 μM at 1.5 μl/min for 60 min). PREP inhibitors had no significant effect on striatal DA levels after systemic administration. JTP-4819 significantly decreased ACh levels both after systemic (by ～25%) and intrastriatal (by ～30-50%) administration. KYP-2047 decreased ACh levels only after intrastriatal administration by retrodialysis (by ～40-50%) when higher drug levels were reached, indicating that higher brain drug levels are needed to modulate ACh levels than to inhibit PREP. This result does not support the earlier hypothesis that the positive cognitive effects of PREP inhibitors in rodents would be mediated through the cholinergic system. In vitro specificity studies did not reveal any obvious off-targets that could explain the observed effect of KYP-2047 and JTP-4819 on ACh levels, instead confirming the concept that these compounds have a high selectivity towards PREP.