Network genealogy of 195-bp satellite DNA supports the superimposed hybridization hypothesis of Trypanosoma cruzi evolutionary pattern

Trypanosoma cruzi is highly diverse genetically and has been partitioned into six discrete typing units (DTUs), recently re-named T. cruzi I-VI. Although T. cruzi reproduces predominantly by binary division, accumulating evidence indicates that particular DTUs are the result of hybridization events. Two major scenarios for the origin of the hybrid lineages have been proposed. It is accepted widely that the most heterozygous TcV and TcVI DTUs are the result of genetic exchange between TcII and TcIII strains. On the other hand, the participation of a TcI parental in the current genome structure of these hybrid strains is a matter of debate. Here, sequences of the T. cruzi-specific 195-bp satellite DNA of TcI, TcII, Tat, TcV, and TcVI strains have been used for inferring network genealogies. The resulting genealogy showed a high degree of reticulation, which is consistent with more than one event of hybridization between the Tc DTUs. The data also strongly suggest that Tat is a hybrid with two distinct sets of satellite sequences, and that genetic exchange between TcI and TcII parentals occurred within the pedigree of the TcV and TcVI DTUs. Although satellite DNAs belong to the fast-evolving portion of eukaryotic genomes, in >100 satellite units of nine T. cruzi strains we found regions that display 100% identity. No DTU-specific consensus motifs were identified, inferring species-wide conservation. (C) 2010 Elsevier B.V. All rights reserved.

Expression Profile of Rat Hippocampal Neurons Treated with the Neuroprotective Compound 2,4-Dinitrophenol: Up-Regulation of cAMP Signaling Genes

2,4-Dinitrophenol (DNP) is classically known as a mitochondrial uncoupler and, at high concentrations, is toxic to a variety of cells. However, it has recently been shown that, at subtoxic concentrations, DNP protects neurons against a variety of insults and promotes neuronal differentiation and neuritogenesis. The molecular and cellular mechanisms underlying the beneficial neuroactive properties of DNP are still largely unknown. We have now used DNA microarray analysis to investigate changes in gene expression in rat hippocampal neurons in culture treated with low micromolar concentrations of DNP. Under conditions that did not affect neuronal viability, high-energy phosphate levels or mitochondrial oxygen consumption, DNP induced up-regulation of 275 genes and down-regulation of 231 genes. Significantly, several up-regulated genes were linked to intracellular cAMP signaling, known to be involved in neurite outgrowth, synaptic plasticity, and neuronal survival. Differential expression of specific genes was validated by quantitative RT-PCR using independent samples. Results shed light on molecular mechanisms underlying neuroprotection by DNP and point to possible targets for development of novel therapeutics for neurodegenerative disorders.

Prion Protein and Its Ligand Stress Inducible Protein 1 Regulate Astrocyte Development

Prion protein (PrP(C)) interaction with stress inducible protein 1 (STI1) mediates neuronal survival and differentiation. However, the function of PrP(C) in astrocytes has not been approached. In this study, we show that STI1 prevents cell death in wild-type astrocytes in a protein kinase A-dependent manner, whereas PrP(C)-null astrocytes were not affected by STI1 treatment. At embryonic day 17, cultured astrocytes and brain extracts derived from PrP(C)-null mice showed a reduced expression of glial fibrillary acidic protein (GFAP) and increased vimentin and nestin expression when compared with wild-type, suggesting a slower rate of astrocyte maturation in PrP(C)-null animals. Furthermore, PrP(C)-null astrocytes treated with STI1 did not differentiate from a flat to a process-bearing morphology, as did wild-type astrocytes. Remarkably, STI1 inhibited proliferation of both wild-type and PrP(C)-null astrocytes in a protein kinase C-dependent manner. Taken together, our data show that PrP(C) and STI1 are essential to astrocyte development and act through distinct signaling pathways.(C) 2009 Wiley-Liss, Inc.

Stoppa skogsmaskinen! : vad krävs för att barn ska samarbeta?

Syftet med den här undersökningen är att undersöka några pedagogers uppfattning om vilka olikafaktorer som kan påverka barns benägenhet att samarbeta och på vilket sätt dessa faktorer påverkar. Sommetod för att samla in data till studien har fyra pedagoger intervjuats. De berättar om i vilka situationerde sett barn samarbeta. Undersökningen redogör för olika faktorer som påverkar barns förmåga attsamarbeta. Dessa är miljön, gruppidentitet, kommunikation, tillit, gemensamt mål samt de vuxnasförhållningssätt. De olika påverkansfaktorerna samverkar med varandra men den övergripande faktornför barn är de vuxnas förhållningssätt då det är detta förhållningssätt som skapar förutsättningarna för deandra faktorerna. Undersökningen tar också upp skillnader mellan pedagoginitierat samarbete ochbarninitierat samarbete samt jämför pedagogernas erfarenhetsbaserade kunskap med denforskningsbaserade kunskapen.

Den Sociala Musikscenen : Intervjuundersökning med musiker och ljudtekniker om deras arbeten med scenframträdanden

Genom en intervjuundersökning med några verksamma ljudtekniker och musiker är syftet med undersökningen att redogöra för viktiga förutsättningar för musikers och ljudteknikers sociala samspel vid scenframträdanden. Problemområdet består av tidigare forskning om musikers och ljudteknikers samspel och arbetsdelning vid inspelningar i studiomiljö. Undersökningens frågeställning är: Vilka förutsättningar för ett socialt samspel anser internationellt aktiva musiker och ljudtekniker vara viktigast under scenframträdanden? Analysen har gjorts med teori om konventioner för konstnärers och hantverkares samspel från Howard Becker (1982) samt hur sociala relationsband stärks i personliga nätverk från Granovetter (1973). Resultatet visar att en bakgrund som musiker var viktigt för ljudteknikerna, medhörning och publikrespons var viktigt för musikerna, samspel kommuniceras med gester och ljudtekniker har idag utökade ansvarsområden än tidigare. Arbetets förutsättningar i och utanför Sverige var liknande när det gällde teknik men skiljer sig på annat sätt. Det sociala samspelet var nödvändigt för ljudteknikernas personliga nätverk. Undersökningens resultat bidrar till kunskapsområdet som är relevant för blivande eller professionella ljudtekniker och musiker för att bidra till vidare undersökningar.

Fred: An approach to generating real, correct, reusable programs from proofs

In this paper we describe our system for automatically extracting "correct" programs from proofs using a development of the Curry-Howard process. Although program extraction has been developed by many authors, our system has a number of novel features designed to make it very easy to use and as close as possible to ordinary mathematical terminology and practice. These features include 1. the use of Henkin's technique to reduce higher-order logic to many-sorted (first-order) logic; 2. the free use of new rules for induction subject to certain conditions; 3. the extensive use of previously programmed (total, recursive) functions; 4. the use of templates to make the reasoning much closer to normal mathematical proofs and 5. a conceptual distinction between the computational type theory (for representing programs)and the logical type theory (for reasoning about programs). As an example of our system we give a constructive proof of the well known theorem that every graph of even parity, which is non-trivial in the sense that it does not consist of isolated vertices, has a cycle. Given such a graph as input, the extracted program produces a cycle as promised.

Protocols between programs and proofs

In this paper we describe a new protocol that we call the Curry-Howard protocol between a theory and the programs extracted from it. This protocol leads to the expansion of the theory and the production of more powerful programs. The methodology we use for automatically extracting “correct” programs from proofs is a development of the well-known Curry-Howard process. Program extraction has been developed by many authors, but our presentation is ultimately aimed at a practical, usable system and has a number of novel features. These include 1. a very simple and natural mimicking of ordinary mathematical practice and likewise the use of established computer programs when we obtain programs from formal proofs, and 2. a conceptual distinction between programs on the one hand, and proofs of theorems that yield programs on the other. An implementation of our methodology is the Fred system. As an example of our protocol we describe a constructive proof of the well-known theorem that every graph of even parity can be decomposed into a list of disjoint cycles. Given such a graph as input, the extracted program produces a list of the (non-trivial) disjoint cycles as promised.

Extraction of structured programs from specification proofs

We present a method using an extended logical system for obtaining programs from specifications written in a sublanguage of CASL. These programs are “correct” in the sense that they satisfy their specifications. The technique we use is to extract programs from proofs in formal logic by techniques due to Curry and Howard. The logical calculus, however, is novel because it adds structural rules corresponding to the standard ways of modifying specifications: translating (renaming), taking unions, and hiding signatures. Although programs extracted by the Curry-Howard process can be very cumbersome, we use a number of simplifications that ensure that the programs extracted are in a language close to a standard high-level programming language. We use this to produce an executable refinement of a given specification and we then provide a method for producing a program module that maximally respects the original structure of the specification. Throughout the paper we demonstrate the technique with a simple example.