A computable expression of closure to efficient causation

In this paper, we propose a mathematical expression of closure to efficient causation in terms of λ-calculus; we argue that this opens up the perspective of developing principled computer simulations of systems closed to efficient causation in an appropriate programming language. An important implication of our formulation is that, by exhibiting an expression in λ-calculus, which is a paradigmatic formalism for computability and programming, we show that there are no conceptual or principled problems in realizing a computer simulation or model of closure to efficient causation. We conclude with a brief discussion of the question whether closure to efficient causation captures all relevant properties of living systems. We suggest that it might not be the case, and that more complex definitions could indeed create crucial some obstacles to computability.     

Simulating Henipavirus Multicycle Replication in a Screening Assay Leads to Identification of a Promising Candidate for Therapy

Nipah (NiV) and Hendra (HeV) viruses are emerging zoonotic paramyxoviruses that cause encephalitis in humans, with fatality rates of up to 75%. We designed a new high-throughput screening (HTS) assay for inhibitors of infection based on envelope glycoprotein pseudotypes. The assay simulates multicycle replication and thus identifies inhibitors that target several stages of the viral life cycle, but it still can be carried out under biosafety level 2 (BSL-2) conditions. These features permit a screen for antivirals for emerging viruses and select agents that otherwise would require BSL-4 HTS facilities. The screening of a small compound library identified several effective molecules, including the well-known compound chloroquine, as highly active inhibitors of pseudotyped virus infection. Chloroquine inhibited infection with live HeV and NiV at a concentration of 1 μM in vitro (50% inhibitory concentration, 2 μM), which is less than the plasma concentrations present in humans receiving chloroquine treatment for malaria. The mechanism for chloroquine''s antiviral action likely is the inhibition of cathepsin L, a cellular enzyme that is essential for the processing of the viral fusion glycoprotein and the maturation of newly budding virions. Without this processing step, virions are not infectious. The identification of a compound that inhibits a known cellular target that is important for viral maturation but that had not previously been shown to have antiviral activity for henipaviruses highlights the validity of this new screening assay. Given the established safety profile and broad experience with chloroquine in humans, the results described here provide an option for treating individuals infected by these deadly viruses.Nipah (NiV) and Hendra (HeV) viruses are newly emerging zoonoses that cause encephalitis in humans, with fatality rates of up to 75% (3, 7, 8, 12, 13, 30). NiV has caused at least nine significant outbreaks in Bangladesh and India since its emergence in Malaysia in 1998 (3, 7, 8, 12, 13, 30). The virus emerged from the fruit bat (flying fox) mammalian reservoir, via the pig, into the human population. However, direct transmission from bats to humans can bypass the pig host, and person-to-person transmission also has now become a primary mode of NiV spread (2, 5). HeV, via the same bat host, has caused disease in horses, with transmission to horse-handlers and veterinarians, and since 1995 has caused sporadic illness in Australia (12). Both viruses, in addition to acute disease, may cause asymptomatic infection in up to 60% of exposed people and may lead to late-onset disease or the relapse of encephalitis years after initial infection (25), as well as persistent or delayed neurological sequelae (11). The vast geographic range of the fruit bat mammalian reservoir raises the possibility of a wide spread of these human diseases, which presently have no clinical treatment or vaccine.The first step in infection with HeV or NiV is binding to the target cells, via the interaction of the viral envelope protein (G) with specific receptor molecules on the cell surface. The receptor for HeV is Ephrin B2 (EFNB2) and for NiV is either EFNB2 or EFNB3 (11). The fusion of the viral envelope with the plasma membrane of the cell is then mediated by the viral fusion protein (F). The F protein is synthesized as a precursor protein (F0) that is proteolytically processed posttranslationally to form a trimer of disulfide-linked heterodimers (F1 + F2). This cleavage event places the fusion peptide at the F1 terminus in the mature F protein and is essential for membrane fusion activity. During viral entry, the fusion peptides, which are buried in the F trimer, must be exposed transiently so that they can insert into the target cell membrane. The conformational change that leads to the exposure of the fusion peptides requires an activation step (22), which is initiated by the interaction of G with its receptor. Only virions bearing the mature, cleaved F can undergo activation and thus are infectious (4, 14, 15).We introduce here a biosafety level 2 (BSL-2)-amenable high-throughput screening (HTS) assay (9) for inhibitors that target several stages of the henipavirus viral cycle, based on envelope glycoprotein pseudotypes. The cell-based assay allows for the simultaneous evaluation of antiviral activity and the cytotoxicity of compounds. We have validated the method with several different classes of henipavirus entry inhibitors as well as protease inhibitors. For this assay, HeV envelope glycoproteins were pseudotyped onto a recombinant vesicular stomatitis virus (VSV) that expresses red fluorescent protein (RFP) but lacks its attachment protein, G (19, 20). The resulting pseudotyped virus bears the HeV binding and fusion proteins. The infection of target cells by pseudotyped virus in the absence and presence of compounds is quantified by assessing the production of red fluorescence. This pseudotyped viral entry assay, unlike previous ones (31), simulates multicycle replication because the monolayer cells, which express viral glycoproteins, will generate more pseudotyped particles when infected. Compounds found to be active in this assay may be those that either block binding, interfere with F activation or fusion, or interfere with the protease processing of F. However, the assay is safe, because these particles can only produce infectious progeny in cells expressing HeV G/F. These features allow experimentation and antiviral assessment for emerging viruses and select agents that otherwise would require BSL-4 HTS facilities. We report the use of this screen to discover effective inhibitors of henipavirus replication and the evaluation of a well-known compound with previously unidentified properties that may allow its immediate use for henipaviruses.     

Reduction screening with endophytic fungi: Synthesis of homochiral secondary alcohols

Twelve strains of endophytic fungi, isolated from various plants (i.e. Eugenia hallii, Schinus molle, Crataegus monogyna, Juniperus communis and Sambucus nigra) sampled in Amazonian forest and in Italy, were screened for their reduction activity with a cocktail of ketones 1–4. The four most active strains [i.e. Phomopsis (FE86 and FE290), Pestalotia and Epicoccum] were chosen for the reduction of 5-hexen-2-one 1, acetophenone 2, cis-bicyclo[3.2.0]hept-2-en-6-one 3, 2-methylcyclohexanone 4, 6-methyl-5-hepten-2-one 5, 2-furyl methyl ketone 6, 1-indanone 7, and 2,4,4-trimethyl-2-cyclohexen-1-one 8 and in all cases the S-alcohols were obtained with variable yields and enantiomeric excesses depending on the strains.     

High-Throughput Genomics Enhances Tomato Breeding Efficiency

Tomato (Solanum lycopersicum) is considered a model plant species for a group of economically important crops, such as potato, pepper, eggplant, since it exhibits a reduced genomic size (950 Mb), a short generation time, and routine transformation technologies. Moreover, it shares with the other Solanaceous plants the same haploid chromosome number and a high level of conserved genomic organization. Finally, many genomic and genetic resources are actually available for tomato, and the sequencing of its genome is in progress. These features make tomato an ideal species for theoretical studies and practical applications in the genomics field. The present review describes how structural genomics assist the selection of new varieties resistant to pathogens that cause damage to this crop. Many molecular markers highly linked to resistance genes and cloned resistance genes are available and could be used for a high-throughput screening of multiresistant varieties. Moreover, a new genomics-assisted breeding approach for improving fruit quality is presented and discussed. It relies on the identification of genetic mechanisms controlling the trait of interest through functional genomics tools. Following this approach, polymorphisms in major gene sequences responsible for variability in the expression of the trait under study are then exploited for tracking simultaneously favourable allele combinations in breeding programs using high-throughput genomic technologies. This aims at pyramiding in the genetic background of commercial cultivars alleles that increase their performances. In conclusion, tomato breeding strategies supported by advanced technologies are expected to target increased productivity and lower costs of improved genotypes even for complex traits.Key Words: Solanum lycopersicum, genetic and genomic resources, molecular markers, microarray, resistance to pathogens, fruit quality.     

Eumalacostracan phylogeny and total evidence: limitations of the usual suspects

Background  

The phylogeny of Eumalacostraca (Crustacea) remains elusive, despite over a century of interest. Recent morphological and molecular phylogenies appear highly incongruent, but this has not been assessed quantitatively. Moreover, 18S rRNA trees show striking branch length differences between species, accompanied by a conspicuous clustering of taxa with similar branch lengths. Surprisingly, previous research found no rate heterogeneity. Hitherto, no phylogenetic analysis of all major eumalacostracan taxa (orders) has either combined evidence from multiple loci, or combined molecular and morphological evidence.     

The Neuropeptide Alpha-Melanocyte-Stimulating Hormone Is Critically Involved in the Development of Cytotoxic CD8+ T Cells in Mice and Humans

Background

The neuropeptide alpha-melanocyte-stimulating hormone is well known as a mediator of skin pigmentation. More recently, it has been shown that alpha-melanocyte-stimulating hormone also plays pivotal roles in energy homeostasis, sexual function, and inflammation or immunomodulation. Alpha-melanocyte-stimulating hormone exerts its antiinflammatory and immunomodulatory effects by binding to the melanocortin-1 receptor, and since T cells are important effectors during immune responses, we investigated the effects of alpha-melanocyte-stimulating hormone on T cell function.

Methodology/Principal Findings

T cells were treated with alpha-melanocyte-stimulating hormone, and subsequently, their phenotype and function was analyzed in a contact allergy as well as a melanoma model. Furthermore, the relevance of alpha-melanocyte-stimulating hormone–mediated signaling for the induction of cytotoxicity was assessed in CD8⁺ T cells from melanoma patients with functional and nonfunctional melanocortin-1 receptors. Here we demonstrate that the melanocortin-1 receptor is expressed by murine as well as human CD8⁺ T cells, and we furthermore show that alpha-melanocyte-stimulating hormone/melanocortin-1 receptor–mediated signaling is critical for the induction of cytotoxicity in human and murine CD8⁺ T cells. Upon adoptive transfer, alpha-melanocyte-stimulating hormone–treated murine CD8⁺ T cells significantly reduced contact allergy responses in recipient mice. Additionally, the presented data indicate that alpha-melanocyte-stimulating hormone via signaling through a functional melanocortin-1 receptor augmented antitumoral immunity by up-regulating the expression of cytotoxic genes and enhancing the cytolytic activity in tumor-specific CD8⁺ T cells.

Conclusions/Significance

Together, these results point to an important role of alpha-melanocyte-stimulating hormone in MHC class I-restricted cytotoxicity. Therefore, treatment of contact allergies or skin cancer with alpha-melanocyte-stimulating hormone or other more stable agonists of melanocortin-1 receptor might ameliorate disease or improve antitumoral immune responses.     

Influenza A viruses in American White Pelican (Pelecanus erythrorhynchos)

The role of many wild waterbird species in the ecology and epidemiology of avian influenza viruses (AIV) remains unclear. We report the first isolation of AIV from American White Pelicans (Pelecanus erythrorhynchos; Pelecaniformes) in North America. Two H13N9 AIVs were isolated from hatchling birds in breeding colonies in Minnesota, USA, during 2007 and 2008. Based on molecular sequencing of the hemagglutinin and neuraminidase genes, the 2008 virus was genetically related to AIVs previously isolated from gulls and shorebirds in North America. The 2007 isolate was most related to AIVs from Eurasian gulls and North American ducks, reflecting both global movement of these viruses and reassortment between viruses associated with duck and gull reservoirs.     

Comprehensive analysis of the major lipid classes in sebum by rapid resolution high-performance liquid chromatography and electrospray mass spectrometry

Sebum is a complex lipid mixture that is synthesized in sebaceous glands and excreted on the skin surface. The purpose of this study was the comprehensive detection of the intact lipids that compose sebum. These lipids exist as a broad range of chemical structures and concentrations. Sebum was collected with SebuTape^TM from the foreheads of healthy donors, and then separated by HPLC on a C8 stationary phase with sub 2 µm particle size. This HPLC method provided high resolution and excellent reproducibility of retention times (RT). Compound mining was performed with time of flight (TOF) and triple quadrupole (QqQ) mass spectrometers (MS), which allowed for the classification of lipids according to their elemental composition, degree of unsaturation, and MS/MS fragmentation. The combination of the two MS systems detected 95 and 29 families of triacylglycerols (TAG) and diacylglycerols (DAG), respectively. Assignment was carried out regardless of positional isomerism. Among the wax esters (WE), 28 species were found to contain the 16:1 fatty acyl moiety. This method was suitable for the simultaneous detection of squalene and its oxygenated derivative. A total of 9 cholesterol esters (CE) were identified and more than 48 free fatty acids (FFA) were detected in normal sebum. The relative abundance of each individual lipid within its own chemical class was determined for 12 healthy donors. In summary, this method provided the first characterization of the features and distribution of intact components of the sebum lipidome.     

Enteric Micro-Particles for Targeted Oral Drug Delivery

This work is focused on production of enteric-coated micro-particles for oral administration, using a water-in-oil-in-water solvent evaporation technique. The active agent theophylline was first encapsulated in cellulose acetate phthalate (CAP), a pH-sensitive well-known polymer, which is insoluble in acid media but dissolves at neutral pH (above pH 6). In this first step, CAP was chosen with the aim optimizing the preparation and characterization methods. The desired release pattern has been obtained (low release at low pH, higher release at neutral pH) but in presence of a low encapsulation efficiency. Then, the CAP was replaced by a novel-synthesized pH-sensitive poly(methyl methacrylate–acrylic acid) copolymer, poly(MMA–AA). In this second step, the role of two process parameters was investigated, i.e., the percentage of emulsion stabilizer (polyvinyl alcohol, PVA) and the stirring power for the double emulsion on the encapsulation efficiency. The encapsulation efficiency was found to increase with PVA percentage and to decrease with the stirring power. By increasing the PVA content and by decreasing the stirring power, a high stable double emulsion was obtained, and this explains the increase in encapsulation efficiency found.