Rapid routes of synthesis of chemically reactive and highly radioactively labeled alpha- and beta-oligonucleotide derivatives for in vivo studies

Development of the antisense oligonucleotide strategy for the regulation of gene expression in vivo poses several problems: the stability of oligonucleotides toward intracellular nucleases, labeling of oligonucleotides with high specific radioactivity, improvements of penetration of oligonucleotides into living cells, and enhancement of antisense action by coupling of chemically active groups. In the present paper synthesis of highly radioactively labeled [32P]- and [35S]oligonucleotide derivatives is described starting from both natural (beta) and nuclease-resistant (alpha) anomers of oligonucleotides. Conditions for preparative phosphorylation and thiophosphorylation suitable for oligonucleotides of various lengths, base composition, and anomeric forms were established. The stability of the phosphoramide bond under in vivo experimental conditions was checked. The methods of terminal phosphate chemical activation and terminal thiophosphate alkylation were applied to synthesize oligonucleotides equipped with hydrophobic, intercalating, alkylating, and photoactivatable groups. In the case of porphyrin-oligonucleotide conjugates, a series of new monofunctional porphyrin derivatives bearing a free aliphatic amino group was developed.     

Building up biogeography: Pattern to process

Linking pattern to process across spatial and temporal scales has been a key goal of the field of biogeography. In January 2017, the 8th biennial conference of the International Biogeography Society sponsored a symposium on Building up biogeography—process to pattern that aimed to review progress towards this goal. Here we present a summary of the symposium, in which we identified promising areas of current research and suggested future research directions. We focus on (1) emerging types of data such as behavioural observations and ancient DNA, (2) how to better incorporate historical data (such as fossils) to move beyond what we term “footprint measures” of past dynamics and (3) the role that novel modelling approaches (e.g. maximum entropy theory of ecology and approximate Bayesian computation) and conceptual frameworks can play in the unification of disciplines. We suggest that the gaps separating pattern and process are shrinking, and that we can better bridge these aspects by considering the dimensions of space and time simultaneously.     

Construction and characterization of a cloned probe for the detection of Phoma tracheiphila in plant tissues

Summary The construction and characterization of the recombinant clone, pPhoB25 is described. This clone contains an highly repeated sequence of DNA from the fungus Phoma tracheiphila, a pathogen of the lemon. The specificity of the probe was determined by molecular hybridization with the DNA of the host plant and with those of several fungi which can be found associated with the lemon plants. The clone was used successfully as a specific and sensitive probe for the detection of the pathogen in infected plant tissues by dotblot hybridization under laboratory and field conditions.     

Optimal functional levels of activation-induced deaminase specifically require the Hsp40 DnaJa1

The enzyme activation-induced deaminase (AID) deaminates deoxycytidine at the immunoglobulin genes, thereby initiating antibody affinity maturation and isotype class switching during immune responses. In contrast, off-target DNA damage caused by AID is oncogenic. Central to balancing immunity and cancer is AID regulation, including the mechanisms determining AID protein levels. We describe a specific functional interaction between AID and the Hsp40 DnaJa1, which provides insight into the function of both proteins. Although both major cytoplasmic type I Hsp40s, DnaJa1 and DnaJa2, are induced upon B-cell activation and interact with AID in vitro, only DnaJa1 overexpression increases AID levels and biological activity in cell lines. Conversely, DnaJa1, but not DnaJa2, depletion reduces AID levels, stability and isotype switching. In vivo, DnaJa1-deficient mice display compromised response to immunization, AID protein and isotype switching levels being reduced by half. Moreover, DnaJa1 farnesylation is required to maintain, and farnesyltransferase inhibition reduces, AID protein levels in B cells. Thus, DnaJa1 is a limiting factor that plays a non-redundant role in the functional stabilization of AID.     

Effects of subinhibitory concentrations of clindamycin on the morphological, biochemical and genetic characteristics of Bacteroides fragilis

The effects of subinhibitory concentrations of clindamycin on the morphological, biochemical and genetic characteristics of species of the Bacteroides fragilis group isolated from children with diarrhea were determined. The minimal inhibitory and subinhibitory concentrations for clindamycin were determined. Minimal inhibitory concentration values ranging from 0.25 to 512 microg mL(-1) were observed. Cultures grown with clindamycin were used to determine the macroscopic morphological characteristics, cellular viability, ultrastructural characteristics and DNA integrity. Clindamycin did not alter colonial morphology, but after 6 h elongated cells were observed. Also, extracellular vesicles and electron-lucent areas inside the cytoplasm were observed. Bacteria treated with clindamycin also showed fragmentation of DNA as determined by electrophoresis. The alterations produced by clindamycin might be indicative of a possible modification of the structures involved in bacterial pathogenesis.     

Biosynthesis and trafficking of seven transmembrane receptor signalling complexes

Recent studies have shown that 7-transmembrane receptors (7TM-Rs), their associated signalling molecules and scaffolding proteins are often constitutively associated under basal conditions. These studies highlight that receptor ontogeny and trafficking are likely to play key roles in the determination of both signalling specificity and efficacy. This review highlights information about how 7TM-Rs and their associated signalling molecules are trafficked to the cell surface as well as other intracellular destinations.     

Interactions between GABA-B1 receptors and Kir 3 inwardly rectifying potassium channels

γ-aminobutyric acid (GABA) is the principal inhibitory neurotransmitter in the mammalian brain. It acts via both ionotropic GABA-A and metabotropic GABA-B receptors. We evaluated the interaction of receptors with members of the inwardly rectifying potassium (Kir 3) channel family, which also play an important role in neuronal transmission and membrane excitability. These channels are functionally regulated by GABA-B receptors. Possible physical interactions between GABA-B receptor and Kir 3 channels expressed in HEK cells were evaluated using Bioluminescence Resonance Energy Transfer (BRET) experiments, co-immunoprecipitation and confocal microscopy. Our data indicate that Kir 3 channels and Gβγ subunits can interact with the GABA-B₁ subunits independently of the GABA-B₂ subunit or Kir 3.4 which are ultimately responsible for their targetting to the cell surface. Thus signalling complexes containing GABA-B receptors, G proteins and Kir channels are formed shortly after biosynthesis most likely in the endoplasmic reticulum.