Selection in Cladocera on the basis of a physiological character

Ohne Zusammenfassung

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Selection in Cladocera on the basis of a physiological character

     

miRNA Regulation of Gene Expression: A Predictive Bioinformatics Analysis in the Postnatally Developing Monkey Hippocampus

Regulation of gene expression in the postnatally developing hippocampus might contribute to the emergence of selective memory function. However, the mechanisms that underlie the co-regulation of expression of hundreds of genes in different cell types at specific ages in distinct hippocampal regions have yet to be elucidated. By performing genome-wide microarray analyses of gene expression in distinct regions of the monkey hippocampal formation during early postnatal development, we identified one particular group of genes exhibiting a down-regulation of expression, between birth and six months of age in CA1 and after one year of age in CA3, to reach expression levels observed at 6-12 years of age. Bioinformatics analyses using NCBI, miRBase, TargetScan, microRNA.org and Affymetrix tools identified a number of miRNAs capable of regulating the expression of these genes simultaneously in different cell types, i.e., in neurons, astrocytes and oligodendrocytes. Interestingly, sixty-five percent of these miRNAs are conserved across species, from rodents to humans; whereas thirty-five percent are specific to primates, including humans. In addition, we found that some genes exhibiting greater down-regulation of their expression were the predicted targets of a greater number of these miRNAs. In sum, miRNAs may play a fundamental role in the co-regulation of gene expression in different cell types. This mechanism is partially conserved across species, and may thus contribute to the similarity of basic hippocampal characteristics across mammals. This mechanism also exhibits a phylogenetic diversity that may contribute to more subtle species differences in hippocampal structure and function observed at the cellular level.     

Altered profile of secondary metabolites in the root exudates of Arabidopsis ATP-binding cassette transporter mutants

Following recent indirect evidence suggesting a role for ATP-binding cassette (ABC) transporters in root exudation of phytochemicals, we identified 25 ABC transporter genes highly expressed in the root cells most likely to be involved in secretion processes. Of these 25 genes, we also selected six full-length ABC transporters and a half-size transporter for in-depth molecular and biochemical analyses. We compared the exuded root phytochemical profiles of these seven ABC transporter mutants to those of the wild type. There were three nonpolar phytochemicals missing in various ABC transporter mutants compared to the wild type when the samples were analyzed by high-performance liquid chromatography-mass spectrometry. These data suggest that more than one ABC transporter can be involved in the secretion of a given phytochemical and that a transporter can be involved in the secretion of more than one secondary metabolite. The primary and secondary metabolites present in the root exudates of the mutants were also analyzed by gas chromatography-mass spectrometry, which allowed for the identification of groups of compounds differentially found in some of the mutants compared to the wild type. For instance, the mutant Atpdr6 secreted a lower level of organic acids and Atmrp2 secreted a higher level of amino acids as compared to the wild type. We conclude that the release of phytochemicals by roots is partially controlled by ABC transporters.     

Seasonal genetic variation associated with population dynamics of a poecilogonous polychaete worm

Poecilogonous species show variation in developmental mode, with larvae that differ both morphologically and ecologically. The spionid polychaete Pygospio elegans shows variation in developmental mode not only between populations, but also seasonally within populations. We investigated the consequences of this developmental polymorphism on the spatial and seasonal genetic structure of P. elegans at four sites in the Danish Isefjord‐Roskilde‐Fjord estuary at six time points, from March 2014 until February 2015. We found genetic differentiation between our sampling sites as well as seasonal differentiation at two of the sites. The seasonal genetic shift correlated with the appearance of new size cohorts in the populations. Additionally, we found that the genetic composition of reproductive individuals did not always reflect the genetic composition of the entire sample, indicating that variance in reproductive success among individuals is a likely explanation for the patterns of chaotic genetic patchiness observed during this and previous studies. The heterogeneous, unpredictable character of the estuary might maintain poecilogony in P. elegans as a bet‐hedging strategy in the Isefjord‐Roskilde‐Fjord complex in comparison with other sites where P. elegans are expected to be fixed to a certain mode of development.     

Effects of adsorbed organic and primary fouling films on bryozoan settlement

Marine primary fouling films, which consist of molecular organic and microbial components, have been reported to facilitate colonization of immersed surfaces by marine fouling organisms. Larvae of the cosmopolitan fouling bryozoan Bugula neritina (Linnaeus) were offered various substrata for attachment and metamorphosis. The materials were offered (a) after detergent washing, (b) after sorption of dissolved organic molecular films, and (c) after formation of primary films consisting of both microbial and adsorbed organic material. Wettability of the substrata by sea water was determined by contact angle measurements for each substratum. On washed substrata, attachment was favored with contact angles greater than ≈45° (cos contact angle <0.7). Adsorbed surface films had no effect on the low settlement of larvae on glass and high settlement on plastics. Microbial primary films, however, made glass attractive and plastics unattractive. These settlement preference changes did not correlate with the changes in wettability observed on these substrata. Dispersion of larvae over the settlement surface was random except on wettable surfaces coated with bacterial films, where settlement was strongly clustered (contagious).     

A plasmid display platform for the selection of peptides exhibiting a functional cell-penetrating phenotype

Cell-penetrating peptides (CPPs) represent a promising nonviral platform for the delivery of therapeutic cargos to cells and tissues. However, these peptides are often nonspecific, and their mechanism of action is still a subject of debate, which hinders the design of new CPPs. The alternative to rational protein design is the combinatorial approach to protein engineering, whereby large libraries of peptides are created and a screening or selection procedure is used to identify members with the desired phenotype(s). Here we describe a novel procedure for selecting peptides with a CPP phenotype using a plasmid display (PD) platform to link the peptides to their encoding DNA sequences. The PD system is based on genetic fusions to a DNA binding domain. The plasmid was designed to concomitantly express a fluorescent reporter protein to serve as a mock therapeutic cargo indicating its functional delivery into a cell. We have demonstrated this selection strategy using a control CPP (the TAT peptide) in the PC12 neuronal-like cell line. In the absence of transfection reagents, TAT was unable to deliver the protein/DNA complexes. The inclusion of the HA2 peptide from the hemagglutinin protein and the addition of polyethylenimine (PEI) were similarly ineffective. The addition of Lipofectamine, however, enabled the TAT-mediated delivery of the protein/DNA complexes, which was significantly better than control experiments without a CPP. This new PD selection platform will be a valuable new approach for use in identifying unique CPPs from randomized libraries with novel abilities and specificities.     

A comprehensive test of the ‘limiting resources’ framework applied to plant tolerance to apical meristem damage

Tolerance to apical meristem damage (AMD) is a form of plant defense against herbivory. Theoretical models come to different conclusions about the effects of inorganic soil nutrient levels on tolerance to AMD, and different plants have shown different relationships between these variables. To assign some order to these disparate patterns and to resolve conflicts among the models, the ‘limiting resources model’ (LRM) was developed. However, we believe that the LRM is actually comprised of several different models, which we describe. Our study marks the first comprehensive and simultaneous test of the entire LRM framework, treating it explicitly as separate models, which also evaluates the models’ underlying assumptions. We studied tolerance to AMD in laboratory‐reared natural populations of Arabidopsis thaliana from three different regions of Europe, spanning a wide latitudinal gradient. We show that, in different populations of this species, basic responses to nutrients and damage are best described by different models, which are based on different assumptions and make different predictions. This demonstrates the need for complexity in our explanations, and suggests that no one existing model can account for all relationships between tolerance to AMD and nutrients. Our results also demonstrate that fruit production can provide a misleading approximation of fitness in A. thaliana, contrary to the common assumption in the literature.     

16S rRNA Gene Survey of Microbial Communities in Winogradsky Columns

A Winogradsky column is a clear glass or plastic column filled with enriched sediment. Over time, microbial communities in the sediment grow in a stratified ecosystem with an oxic top layer and anoxic sub-surface layers. Winogradsky columns have been used extensively to demonstrate microbial nutrient cycling and metabolic diversity in undergraduate microbiology labs. In this study, we used high-throughput 16s rRNA gene sequencing to investigate the microbial diversity of Winogradsky columns. Specifically, we tested the impact of sediment source, supplemental cellulose source, and depth within the column, on microbial community structure. We found that the Winogradsky columns were highly diverse communities but are dominated by three phyla: Proteobacteria, Bacteroidetes, and Firmicutes. The community is structured by a founding population dependent on the source of sediment used to prepare the columns and is differentiated by depth within the column. Numerous biomarkers were identified distinguishing sample depth, including Cyanobacteria, Alphaproteobacteria, and Betaproteobacteria as biomarkers of the soil-water interface, and Clostridia as a biomarker of the deepest depth. Supplemental cellulose source impacted community structure but less strongly than depth and sediment source. In columns dominated by Firmicutes, the family Peptococcaceae was the most abundant sulfate reducer, while in columns abundant in Proteobacteria, several Deltaproteobacteria families, including Desulfobacteraceae, were found, showing that different taxonomic groups carry out sulfur cycling in different columns. This study brings this historical method for enrichment culture of chemolithotrophs and other soil bacteria into the modern era of microbiology and demonstrates the potential of the Winogradsky column as a model system for investigating the effect of environmental variables on soil microbial communities.