Genetic Program of Neuronal Differentiation and Growth Induced by Specific Activation of NMDA Receptors

Glutamate and its receptors are expressed very early during development and may play important roles in neurogenesis, synapse formation and brain wiring. The levels of glutamate and activity of its receptors can be influenced by exogenous factors, leading to neurodevelopmental disorders. To investigate the role of NMDA receptors on gene regulation in a neuronal model, we used primary neuronal cultures developed from embryonic rat cerebri in serum-free medium. Using Affymetrix Gene Arrays, we found that genes known to be involved in neuronal plasticity were differentially expressed 24 h after a brief activation of NMDA receptors. The upregulation of these genes was accompanied by a sustained induction of CREB phosphorylation, and an increase in synaptophysin immunoreactivity. We conclude that NMDA receptor activation elicits expression of genes whose downstream products are involved in the regulation of early phases of the process leading to synaptogenesis and its consolidation, at least in part through sustained CREB phosphorylation. Special issue dedicated to Dr. Anthony Campagnoni.     

Aggregation risk prediction for antibodies and its application to biotherapeutic development

Aggregation is a common problem affecting biopharmaceutical development that can have a significant effect on the quality of the product, as well as the safety to patients, particularly because of the increased risk of immune reactions. Here, we describe a new high-throughput screening algorithm developed to classify antibody molecules based on their propensity to aggregate. The tool, constructed and validated on experimental aggregation data for over 500 antibodies, is able to discern molecules with a high aggregation propensity as defined by experimental criteria relevant to bioprocessing and manufacturing of these molecules. Furthermore, we show how this tool can be combined with other computational approaches during early drug development to select molecules with reduced risk of aggregation and optimal developability properties.     

Protein phosphatase 2A regulatory subunits affecting plant innate immunity,energy metabolism,and flowering time – joint functions among B'η subfamily members

Protein phosphatase 2A (PP2A) is a heterotrimeric complex comprising a catalytic, scaffolding, and regulatory subunit. The regulatory subunits are essential for substrate specificity and localization of the complex and are classified into B/B55, B'', and B” non-related families in higher plants. In Arabidopsis thaliana, the close paralogs B''η, B''θ, B''γ, and B''ζ were further classified into a subfamily of B'' called B''η. Here we present results that consolidate the evidence for a role of the B''η subfamily in regulation of innate immunity, energy metabolism and flowering time. Proliferation of the virulent Pseudomonas syringae in B''θ knockout mutant decreased in comparison with wild type plants. Additionally, B''θ knockout plants were delayed in flowering, and this phenotype was supported by high expression of FLC (FLOWERING LOCUS C). B''ζ knockout seedlings showed growth retardation on sucrose-free medium, indicating a role for B''ζ in energy metabolism. This work provides insight into functions of the B''η subfamily members, highlighting their regulation of shared physiological traits while localizing to distinct cellular compartments.     

A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database

mtcPTM is an online repository of human and mouse phosphosites in which data are hierarchically organized to preserve biologically relevant experimental information, thus allowing straightforward comparisons of phosphorylation patterns found under different conditions. The database also contains the largest available collection of atomic models of phosphorylatable proteins. Detailed analysis of this structural dataset reveals that phosphorylation sites are found in a heterogeneous range of structural and sequence contexts. mtcPTM is available on the web .     

Performance of crosses among flint maize populations under infestation by Sesamia nonagrioides (Lepidoptera: Noctuidae)

Flint maize, Zea mays L., varieties provide some interesting agronomic characteristics and kernels that possess a better ability than other kernels for developing high-quality flour. The pink stem borer, Sesamia nonagrioides Lefebvre, is an important constraint for the maize crop in Mediterranean regions. The objective of this work was to identify a "flint x flint" heterotic pattern that would perform well under artificial infestation by S. nonagrioides. A 10-population diallel was evaluated under infestation by S. nonagrioides in 2 yr. Variety effects were the only significant effects involved in stem and ear resistance to S. nonagrioides attack. Variety effects and average heterosis effects were the only significant effects for grain yield under artificial infestation conditions. Considering variety effects and cross-performance, the heterotic pattern Basto/Enano levantixo x Longfellow (BA/EL x LO) would be recommended for obtaining flint maize hybrids tolerant to S. nonagrioides attack because BA/EL had the most favorable variety effects for stem resistance, LO exhibited the most positive variety effects for grain yield, and the cross BA/EL x LO yielded significantly more than the remaining crosses.     

Phylogenetic analyses of the rbcL sequences from haptophytes and heterokont algae suggest their chloroplasts are unrelated

Using the large subunit of RuBisCo (rbcL) sequences from cyanobacteria, proteobacteria, and diverse groups of algae and green plants, we evaluated the plastid relationship between haptophytes and heterokont algae. The rbcL sequences were determined from three taxa of heterokont algae (Bumilleriopsis filiformis, Pelagomonas calceolata, and Pseudopedinella elastica) and added to 25 published sequences to obtain a data set comprising 1,434 unambiguously aligned sites (approximately 98% of the total rbcL gene). Higher levels of mutational saturation in third codon positions were observed by plotting the pairwise substitutions with and without corrections for multiple substitutions at the same site for first and second codon positions only and for third positions only. In accordance with this finding phylogeny reconstructions were completed by omitting third codon positions, thus using 956 bp in weighted-parsimony and maximum-likelihood analyses. The midpoint-rooted phylogenies showed two major clusters, one containing cyanobacteria, glaucocystophytes, a phototrophic euglenoid, chlorophytes, and embryophytes (the green lineage), the other containing proteobacteria, haptophytes, red algae, a cryptophyte, and heterokont algae (the non-green lineage). In the nongreen lineage, the haptophytes formed a sister group to the clade containing heterokont algae, red algae, and the cryptophyte Guillardia theta. This branching pattern was well supported in terms of bootstrap values in weighted- parsimony and maximum-likelihood analyses (100% and 92%, respectively). However, the phylogenetic relationship among red algae, heterokonts, and a cryptophyte taxon was not especially well resolved. A four- cluster analysis was performed to further explore the statistical significance of the relationship between proteobacteria, red algae (including and excluding Guillardia theta), haptophytes, and heterokont algae. This test strongly favored the hypothesis that the heterokonts and red algae are more closely related to each other than either is to proteobacteria or haptophytes. Hence, this molecular study based on a plastid-encoded gene provides additional evidence for a distant relationship between haptophytes and the heterokont algae. It suggests an evolutionary scenario in which the ancestor of the haptophyte lineage engulfed a phototrophic eukaryote and, more recently, the heterokont lineage became phototrophic by engulfing a red alga.      

Variation in the harvest index of tropical maize: evaluation of recent evidence from Mexico and Malawi

In temperate zones, the potential grain yield of wheat has increased during the twentieth century owing to progressive increases in the harvest index of new varieties, which are principally associated with reduction in plant stature. Crop biomass has not increased substantially. In contrast, the potential grain yield of maize in the USA has increased owing to progressive increases in biomass, principally associated with selection for grain yield at higher population density. Harvest index was already around 0.5 for recommended varieties in 1930, and has not increased significantly since. However, for both crops, the harvest index of a given variety has proved to be a highly‐heritable character, except under severe stress. Less is known about the physiology of tropical maize. This paper reviews evidence from Mexico and Malawi that tropical maize can respond to selection for reduced stature following the same pattern as temperate wheat, but, under other circumstances, the magnitude of harvest index is not highly heritable, varying inconsistently with season, management and environment. It is proposed that these differences arise out of the unique vulnerability of the grain‐setting process around flowering. The plasticity of harvest index under long, favourable conditions, however, remains to be explained, although it is probably also related to the events around grain setting. Nevertheless, to the subsistence farmer, higher harvest index may not be a high priority in crop improvement, because of the need for large quantities of high‐quality stover.     

Morphological Constraints of Shoot Demography of a Clonal Plant: Extra- and Intravaginal Tillers of Festuca rubra

Abstract Festuca rubra forms tillers in two different ways: extravaginally and intravaginally. Demography of these two tiller types was observed in seventeen selected tussocks of Festuca rubra s.s. over four growing seasons. Extravaginal tillers were bigger at birth and on the average produced twice as many daughter tillers per tiller. In general, the natality and mortality of extravaginal tillers were less regular than that of intravaginal tillers. Overall tillering rate per tiller was correlated with the density of the surrounding vegetation; mortality, natality and tiller life span were not. High density of the surrounding vegetation did not result in increased formation of extravaginal tillers. The proportion of the extravaginal tillers was not correlated with the density of the F. rubra tussocks. There is no evidence for foraging by extravaginal tillers, but they do act as founders of small clusters of tillers.     

Tn5401 disruption of the spo0F gene, identified by direct chromosomal sequencing, results in CryIIIA overproduction in Bacillus thuringiensis.

The Bacillus thuringiensis spo0F gene was identified by chromosomal DNA sequencing of sporulation mutants derived from a B. thuringiensis transposon insertion library. A spo0F defect in B. thuringiensis, which was suppressed by multicopy hknA or kinA, resulted in the overproduction of the CryIIIA insecticidal crystal protein.     

Distribution and conservation of mobile elements in the genus Drosophila

Essentially nothing is known of the origin, mode of transmission, and evolution of mobile elements within the genus Drosophila. To better understand the evolutionary history of these mobile elements, we examined the distribution and conservation of homologues to the P, I, gypsy, copia, and F elements in 34 Drosophila species from three subgenera. Probes specific for each element were prepared from D. melanogaster and hybridized to genomic DNA. Filters were washed under conditions of increasing stringency to estimate the similarity between D. melanogaster sequences and their homologues in other species. The I element homologues show the most limited distribution of all elements tested, being restricted to the melanogaster species group. The P elements are found in many members of the subgenus Sophophora but, with the notable exception of D. nasuta, are not found in the other two subgenera. Copia-, gypsy-, and F-element homologues are widespread in the genus, but their similarity to the D. melanogaster probe differs markedly between species. The distribution of copia and P elements and the conservation of the gypsy and P elements is inconsistent with a model that postulates a single ancient origin for each type of element followed by mating-dependent transmission. The data can be explained by horizontal transmission of mobile elements between reproductively isolated species.