Soporte de sistema operativo para ahorro de energía en plataformas móviles con procesadores multicore asimétricos

Los procesadores multicore asimétricos con repertorio común de instrucciones (AMPsAsymmetric Multicore Processors) han sido propuestos recientemente como alternativa de bajo consumo a los procesadores multicore simétricos convencionales. Los AMPs combinan, en un mismo chip, cores rápidos de alto rendimiento, con cores más lentos y sencillos de consumo reducido. Uno de los ejemplos más destacados de procesador multicore asimétrico es el procesador big.LITTLE de ARM, que incorporan algunos modelos de teléfonos móviles y tablets disponibles en la actualidad. Trabajos previos han demostrado que para explotar los beneficios potenciales de los procesadores multicore asimétricos, el sistema operativo debe tener en cuenta el beneficio relativo (speedup) que cada aplicación experimenta al ejecutar en un core rápido frente a un core lento. Actualmente, los planificadores por defecto de los sistemas operativos de propósito general no tienen en cuenta la diversidad de speedups entre aplicaciones que puede estar presente en una carga de trabajo multiprogramada. En consecuencia, la asignación de aplicaciones a cores que hacen estos planificadores no extrae el máximo rendimiento por vatio de la plataforma. Recientemente se han realizado extensiones en el kernel Linux para ofrecer un mejor soporte de planificación en multicore asimétricos. Sin embargo, estas extensiones del planificador, utilizadas fundamentalmente en dispositivos móviles con el sistema operativo Android, tampoco tienen en cuenta la diversidad de speedups en las aplicaciones de la carga de trabajo. Por lo tanto estas extensiones no constituyen una aproximación robusta desde el punto de vista de la eficiencia energética. En este proyecto se lleva a cabo la evaluación exhaustiva de distintos algoritmos de planificación para multicore asimétricos sobre una plataforma provista de un procesador ARM big.LITTLE. El principal objetivo del estudio es cuantificar el grado de eficiencia energética y el rendimiento global proporcionado por implementaciones de estos algoritmos en el kernel Linux sobre hardware multicore asimétrico real.

Identification and bioactivity evaluation of two novel temporins from the skin secretion of the European edible frog, Pelophylax kl. Esculentus

The amphibian temporins, amongst the smallest antimicrobial peptides (AMPs), are α-helical, amphipathic, hydrophobic and cationic and are active mainly against Gram-positive bacteria but inactive or weakly active against Gram-negative bacteria. Here, we report two novel members of the temporin family, named temporin-1Ee (FLPVIAGVLSKLFamide) and temporin-1Re (FLPGLLAGLLamide), whose biosynthetic precursor structures were deduced from clones obtained from skin secretion-derived cDNA libraries of the European edible frog, Pelophylax kl. esculentus, by ‘shotgun’ cloning. Deduction of the molecular masses of each mature processed peptide from respective cloned cDNAs was used to locate respective molecules in reverse-phase HPLC fractions of secretion. Temporin-1Ee (MIC = 10 μM) and temporin-1Re (MIC = 60 μM) were both found to be active against Gram-positive Staphylococcus aureus, but retaining a weak haemolytic activity. To our knowledge, Single-site substitutions can dramatically change the spectrum of activity of a given temporin. Compared with temporine-1Ec, just one chemically-conservative substitution (Val8 instead of Leu8), temporin-1Ee bearing a net charge of +2 displays broad-spectrum activity with particularly high potency on the clinically relevant Gram-negative strains, Escherichia coli (MIC = 40 μM). These factors bode well for translating temporins to be potential drug candidates for the design of new and valuable anti-infective agents.

Molecular and Functional Characterization of Antimicrobial Peptides in Crustaceans

Most living organisms are constantly exposed to potentially harmful pathogens. It is the immune system of the organism that enables it to survive in an environment loaded with dangerous pathogenic microorganisms. The innate immunity provides organisms with a rapid and non-specific first line of defense against pathogens. It includes physical barriers such as skin and mucous membranes and chemical barriers including the high acidity of gastric juice, and specialized soluble molecules that possess antimicrobial activity. One of the well-known innate immune defense mechanisms is the production of antimicrobial substances by specific cells or tissues of the organisms. Antimicrobial peptides (AMPs) are such natural substances that

Molecular and Functional Characterization of Histone Derived Antimicrobial Peptides from Marine Organisms

Antimicrobial peptides (AMPs) are gene encoded, small sized, generally cationic, amphiphathic peptides characterized by antimicrobial activity against bacteria, fungi, viruses and other pathogens. They are a major component of the innate immune defense system of almost all living organisms, ranging from bacteria to humans and represent the first line of defense against the invading microbial pathogens (Boman, 1995; Zasloff, 2002). Antimicrobial peptides represent a heterogeneous group displaying multiple modes of action that are determined by the sequence and concentration of peptides. Their remarkable specificity for prokaryotes with low toxicity for eukaryotic cells has favored their investigation and exploitation as new antibiotics

Applicazione di un protocollo di screening differenziale nel sistema Vitis vinifera per l’identificazione di peptidi con attività antimicrobica

Le piante e gli animali presentano elementi comuni nel loro sistema di difesa contro gli agenti patogeni, come la sintesi diretta di enzimi idrolitici (chitinasi, glucanasi, proteinasi e ossidasi) e di peptidi antimicrobici (AMPs). Gli AMPs sono peptidi ampiamente espressi negli organismi animali (vertebrati e invertebrati) e nelle piante. Possono essere espressi costitutivamente o rapidamente indotti inseguito ad uno stimolo biotico, a differenti livelli cellulari, per interagire direttamente con l’agente infettante e/o per modulare la risposta immunitaria contro i patogeni. Tali peptidi sono oggi classificati in relazione alle loro caratteristiche biochimiche (carica netta) e/ o alle loro caratteristiche strutturali (composizione amminoacidica, struttura lineare o circolare). In base a queste caratteristiche le molecole possono essere distinte nei seguenti gruppi: 1) peptidi lineari ad alfa elica; 2) peptidi ciclici con β-sheets e due o più ponti disolfuro; 3) peptidi con alfa elica e β-sheets stabilizzati da ponti disolfuro; 4) peptidi con hairpin o loop stabilizzati da ponti disolfuro; 5) peptidi lineari con residui aminoacidici ripetuti, come prolina, glicina, triptofano o istidina; 6) piccoli peptidi con struttura avvolta o con una struttura secondaria non definita. Nonostante la loro diversità strutturale, i peptidi antimicrobici presentano la caratteristica comune di inibire la crescita di un largo spettro di microbi, quali Gram-positivi, Gram-negativi, funghi e in alcuni casi anche virus, tanto da far coniare il termine di “antibiotici naturali”. Negli ultimi anni è notevolmente incrementato l’interesse verso tali peptidi dal momento che dati scientifici hanno mostrato che questi non inducono lo sviluppo di meccanismi di resistenza nei microrganismi patogeni. Gli AMPs quindi potrebbero costituire una valida alternativa non solo in ambito sanitario, per la sostituzione di antibiotici di sintesi chimica e di origine microbiologica, ma potrebbero avere un importante utilizzo in campo industriale e nello sviluppo di nuovi sistemi di conservazione degli alimenti al fine di incrementare la loro “shelf-life”.

Rearing effect of biofloc on antioxidant and antimicrobial transcriptional response in Litopenaeus stylirostris shrimp facing an experimental sub-lethal hydrogen peroxide stress

This study compares the antioxidant and antimicrobial transcriptional expression of blue shrimps reared according to two different systems, BioFloc Technology (BFT) and Clear sea Water (CW) and their differential responses when facing an experimental sublethal hydrogen peroxide stress. After 30 days of rearing, juvenile shrimps were exposed to H2O2 stress at a concentration of 30 ppm during 6 hours. The oxidative stress caused by H2O2 was examined in the digestive glands of the shrimp, in which antioxidant enzyme (AOE) and antimicrobial peptide (AMP) gene expression were analysed by quantitative real-time PCR. Results showed that rearing conditions did not affect the expression of genes encoding AOEs or AMPs. However, H2O2 stress induced a differential response in expression between shrimps from the two rearing treatments (BFT and CW). Comparative analysis of the expression profiles indicates that catalase transcripts were significantly upregulated by H2O2 stress for BFT shrimps while no change was observed for CW shrimps. In contrast, H2O2 caused down-regulation of superoxide dismutase and glutathione transferase transcripts and of the three AMP transcripts studied (penaeidin 2 and 3, and crustin) for CW shrimps, while no effect was observed on BFT shrimp transcript levels. These results suggested that BFT shrimps maintained antioxidant and AMP responses after stress and therefore can effectively protect their cells against oxidative stress, while CW shrimp immune competence seems to decrease after stress.

An intimate link between antimicrobial peptide sequence diversity and binding to essential components of bacterial membranes

Antimicrobial peptides and proteins (AMPs) are widespread in the living kingdom. They are key effectors of defense reactions and mediators of competitions between organisms. They are often cationic and amphiphilic, which favors their interactions with the anionic membranes of microorganisms. Several AMP families do not directly alter membrane integrity but rather target conserved components of the bacterial membranes in a process that provides them with potent and specific antimicrobial activities. Thus, lipopolysaccharides (LPS), lipoteichoic acids (LTA) or the peptidoglycan precursor Lipid II are targeted by a broad series of AMPs. Studying the functional diversity of immune effectors tells us about the essential residues involved in AMP mechanism of action. Marine invertebrates have been found to produce a remarkable diversity of AMPs. Molluscan defensins and crustacean anti-LPS factors (ALF) are diverse in terms of amino acid sequence and show contrasted phenotypes in terms of antimicrobial activity. Their activity is directed essentially against Gram-positive or Gram-negative bacteria due their specific interactions with Lipid II or Lipid A, respectively. Through those interesting examples, we discuss here how sequence diversity generated throughout evolution informs us on residues required for essential molecular interaction at the bacterial membranes and subsequent antibacterial activity. Through the analysis of molecular variants having lost antibacterial activity or shaped novel functions, we also discuss the molecular bases of functional divergence in AMPs.

Lipid-Based Liquid Crystals As Carriers for Antimicrobial Peptides: Phase Behavior and Antimicrobial Effect

International audience

Análise do transcriptoma das glândulas venenosas do escorpião Tityus stigmurus

In Brazil, accidents with scorpions are considered of medical importance, not only by the high incidence, but also for the potentiality of the venom from some species in determining severe clinical conditions. Tityus stigmurus is a widely distributed scorpion species in Northeastern Brazil and known to cause severe human envenomations, inducing pain, hyposthesia, edema, erythema, paresthesia, headaches and vomiting. The present study uses a transcriptomic approach to characterize the molecular repertoire from the non-stimulated venom gland of Tityus stigmurus scorpion. A cDNA library was constructed and 540 clones were sequenced and grouped into 37 clusters, with more than one EST (expressed sequence tag) and 116 singlets. Forty-one percent of ESTs belong to recognized toxin-coding sequences, with antimicrobial toxins (AMP-like) the most abundant transcripts, followed by alfa KTx- like, beta KTx-like, beta NaTx-like and alfa NaTx-like. Our analysis indicated that 34% include other possible venom molecules , whose transcripts correspond to anionic peptides, hypothetical secreted peptides, metalloproteinases, cystein-rich peptides and lectins. Fifteen percent of ESTs are similar to cellular transcripts. Sequences without good matches corresponded to 11%. This investigation provides the first global view of cDNAs from Tityus stigmurus. This approach enables characterization of a large number of venom gland component molecules, which belong either to known or atypical types of venom peptides and proteins from the Buthidae family

Síntese química e avaliação das propriedades antibacterianas e antiparasitárias de análogos de peptídeos antimicrobianos de anuros

Tese (doutorado)—Universidade de Brasília, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Biologia Molecular, 2015.

Molecular dynamics study of a dual-cation ionomer electrolyte

The poly(N1222)xLi1-x[AMPS] ionomer system with dual cations has previously shown decoupled Li ion dynamics from polymer segmental motions, characterized by the glass transition temperature, which can result in a conductive electrolyte material whilst retaining an appropriate modulus (ie. stiffness) so that it can suppress dendrite formation, thereby improving safety when used in lithium metal batteries. To understand this ion dynamics behavior, molecular dynamics techniques have been used in this work to simulate structure and dynamics in these materials. These simulations confirm that the Li ion transport is decoupled from the polymer particularly at intermediate N1222+ concentrations. At 50 mol% N1222+ concentration the polymer backbone is more rigid than for higher N1222+ concentrations, but with increasing temperature Li ion transport is more significant than polymer or quaternary ammonium cation motions. Here we suggest an ion hopping mechanism for Li+, arising from structural rearrangement of ionic clusters that could explain its decoupled behavior. Higher temperatures favor an aggregated ionic structure as well as enhancing these hopping motions. The simulations discussed here provide an atomic-level understanding of ion dynamics that could contribute to designing an improved ionomer with fast ion transport and mechanical robustness.