Engineering genetic circuits: advancements in genetic design automation tools and standards for synthetic biology

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Motifier: An IgOme Profiler Based on Peptide Motifs Using Machine Learning

Antibodies provide a comprehensive record of the encounters with threats and insults to the immune system. The ability to examine the repertoire of antibodies in serum and discover those that best represent “discriminating features” characteristic of various clinical situations, is potentially very useful. Recently, phage display technologies combined with Next-Generation Sequencing (NGS) produced a powerful experimental methodology, coined “Deep-Panning”, in which the spectrum of serum antibodies is probed. In order to extract meaningful biological insights from the tens of millions of affinity-selected peptides generated by Deep-Panning, advanced bioinformatics algorithms are a must. In this study, we describe Motifier, a computational pipeline comprised of a set of algorithms that systematically generates discriminatory peptide motifs based on the affinity-selected peptides identified by Deep-Panning. These motifs are shown to effectively characterize antibody binding activities and through the implementation of machine-learning protocols are shown to accurately classify complex antibody mixtures representing various biological conditions.     

Effect of photoperiod and temperature on the development of frost hardiness in three Alnus species

The influence of short day and low temperature on cold acclimation of A. crispa (Ait.) Pursh, A. glutinosa (L.) Gaertn. and A. rubra Bong, was investigated. Two clones of each species originating from in vitro propagation were exposed to three daylength/temperature treatments. Periodically plantlets were exposed to controlled freezing temperature in order to evaluate their level of frost hardiness.
Short day (SD) and cold temperature (CT) and long day (LD) and cold temperature (CT) were the most effective treatments for the development of frost hardiness in shoots and roots of the three species tested. Short day (SD) and warm temperature (WT) induced a significant increase in hardiness in shoots of all three species. However, this treatment did not trigger root hardening. A. crispa was found to be the hardiest species followed by A. glutinosa and A. rubra . Intraspecific variation was observed between the two A. glutinosa clones. A glutinosa clone AG8, a Russian provenance, showed a greater freezing resistance than A. glutinosa clone AG2, a German provenance.     

Lymphocyte clones from old subjects: growing rate and functional activity

Old subjects exhibit a decline in circulating T cells and an impaired proliferative response to mitogens, plus a relative increase in cells with NK phenotype not associated with a concomitant increase in their cytolitic activity.In the present study a limiting dilution assay was used to evaluate the phenotype, the functional activity and the proliferative capacity of clones obtained from peripheral blood lymphocytes of old and young subjects. CD5+ CD8+ clones from old people showed a significant impairment in their proliferative capacity and a decreased lytic activity against K562 and P815-IgG cell lines.     

Glutamate Dehydrogenase Activity Is Markedly Higher in a "Golgi-Bergmann"-Like Glial Clone than in Other Astroglial Cell Lines

Glutamate appears to be the neurotransmitter of granule cells, the major neuronal population of the cerebellar cortex. To determine the role of astroglial cells in the synthesis of glutamate, we have measured the specific activity of glutamate dehydrogenase (GDH) in clonal cell lines that might be the in vitro equivalents of the different cerebellum astroglial cell types. In conditions where GDH operates in the direction of glutamate synthesis, the specific activity of GDH measured in the "Golgi-Bergmann"-like clone was 4-6 times higher than in the "velate protoplasmic"- or "fibrous-like" astrocytic clones. These data correlate well with the intense immunoreactivity to GDH in Golgi-Bergmann astrocytes in vivo that has been recently reported.     

Expression and stability of amplified genes encoding 5-enolpyruvylshikimate-3-phosphate synthase in glyphosate-tolerant tobacco cells

Two distinct cDNAs for 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) were obtained from a glyphosate-tolerant tobacco cell line. The cDNAs were 89% identical and the predicted sequences of the mature proteins were greater than 83% identical with EPSPS proteins from other plants. Tobacco EPSPS proteins were more similar to those from tomato and petunia than Arabidopsis. One cDNA clone, EPSPS-1, represented a gene that was amplified in glyphosate-tolerant cells, while the gene for EPSPS-2 was unaltered in these cells. Consequently, EPSPS-1 mRNA was more abundant in tolerant than unselected cells, whereas EPSPS-2 mRNA was at relatively constant levels in these cell lines. Exposure of unselected cells and tobacco leaves to glyphosate produced a transient increase in EPSPS mRNA. However, glyphosate-tolerant cells containing amplified copies of EPSPS genes did not show a similar response following exposure to glyphosate. A significant proportion of the EPSPS gene amplification was maintained when tolerant cells were grown in the absence of glyphosate for eight months. Plants regenerated from these cells also contained amplified EPSPS genes.     

Isolation and Sequencing of a Genomic Clone for Mouse Brain Specific Small RNA

We isolated a mouse genomic clone that hybridized with small RNA present in the cytoplasm of the brain. The RNA was about 150 nucleotides long. This RNA seemed to be specific to the brain, since it was not found in the liver or kidney. The clone DNA contained a sequence homologous to 82-nucleotide "identifier" core sequence of cDNA clones of rat. The sequence contained a split promoter for RNA polymerase III and was flanked by a 12-nucleotide direct repeat (ATAAATAATTTA).