Cobalt mapping of the nervous system: evidence that cobalt can cross a neuronal membrane

Exposing intact nerves of Aplysia to exogenous CoCl2 was sufficient to fill neurons by axonal iontophoresis. There were no significant differences between filling intact nerves and nerves whose ends had been cut. Nonneuronal elements were not filled appreciably. These results show that Co2+ can cross intact axonal membranes and suggest that in tracing neuronal pathways Co2+ may not remain confined to neurons whose interiors are directly exposed to it.     

Conditioned genome reconstruction: how to avoid choosing the conditioning genome

Genome phylogenies can be inferred from data on the presence and absence of genes across taxa. Logdet distances may be a good method, because they allow expected genome size to vary across the tree. Recently, Lake and Rivera proposed conditioned genome reconstruction (calculation of logdet distances using only those genes present in a conditioning genome) to deal with unobservable genes that are absent from every taxon of interest. We prove that their method can consistently estimate the topology for almost any choice of conditioning genome. Nevertheless, the choice of conditioning genome is important for small samples. For real bacterial genome data, different choices of conditioning genome can result in strong bootstrap support for different tree topologies. To overcome this problem, we developed supertree methods that combine information from all choices of conditioning genome. One of these methods, based on the BIONJ algorithm, performs well on simulated data and may have applications to other supertree problems. However, an analysis of 40 bacterial genomes using this method supports an incorrect clade of parasites. This is a common feature of model-based gene content methods and is due to parallel gene loss.     

Sliding-end-labelling. A method to avoid artifacts in nucleosome positioning

A method, termed 'sliding-end-labelling', has been devised to avoid a frequent artifact in nucleosome positioning by indirect end labelling, namely the appearing of DNA fragments originated by two nuclease cuts, one of them lying within the region covered by the probe. The method is applied to the nucleosome positioning in the yeast SUC2 gene for invertase.     

Why and how to avoid stenting during brachytherapy

Intracoronary radiation is a promising therapy to reduce restenosis after percutaneous coronary intervention. It may be anticipated that radiation and intracoronary stents - the current standard coronary revascularization procedure - have a synergic antirestenosis effect. However, this potential benefit has not been proven in the clinical scenario. Indeed, this combined approach (stenting plus brachytherapy) may even be harmful. Delayed endothelialization and late stent malapposition are important drawbacks of implanting a metallic prosthesis in the setting of radiation therapy. Owing to the relatively high frequency of late thrombosis after stenting irradiated coronary arteries, the Food and Drug Administration required that the labeling of both gamma- and beta-radiation devices recently approved for clinical use explicitly advise avoidance of the placement of new stents. The pathophysiologic aspects as well as the clinical implications of the implantation of a new stent in association with radiation delivered by radioactive stents or catheter-based systems are discussed in this paper.     

Are Ranvier's nodes of the central nervous system also artifacts by preparation?

Recent research on peripheral nerves of six species of vertebrates concluded that Ranvier's nodes may be artifacts by preparation. As a consequence, the question as to whether or not Ranvier's nodes of the central nervous system may also be artifacts was logically raised. The ultrastructural data concerning our field of research (the cerebellar cortex) support the notion that Ranvier's nodes are real features in the central nervous system; otherwise, the occurrence of vesicular outpockets establishing, along myelinated axons, well conspicuous en passant nodal synapses cannot be explained.     

Quantitative analysis of lateral root development: pitfalls and how to avoid them

The advent of the postgenomics era has led to increased interest in exploring the role of gene networks and signaling pathways in controlling plant development. The last two decades have seen a particular increase in the number of studies focusing on the development of the Arabidopsis thaliana root system. However, the investigation of such a seemingly simple system as an Arabidopsis root can lead to problems in quantification and errors in interpretation if knowledge of root organization is lacking. In this article, we identify a number of these problems and give examples of potentially erroneous and correct determinations of lateral root parameters. Our aim is to bring this important issue to the attention of the plant science community and to suggest ways in which the problems inherent in quantifying the process of lateral root development can be avoided.     

Vaccines,emerging viruses,and how to avoid disaster

Rino Rappuoli is a graduate of Siena University, where he also earned his PhD before moving to the Sclavo Research Center, the Italian vaccine institute, also in Siena. He then spent two years in the USA, mostly at Harvard with John Murphy and Alwin Pappenheimer working on a new diphtheria vaccine based on a non-toxic mutant of diphtheria toxin which has since become the basis for conjugate vaccines against haemophilus, meningococcus, and pneumococcal infections, before returning to the Sclavo Research Center where he developed an acellular vaccine based on a mutant pertussis toxin. With many achievements in vaccine development to his credit, he is now Global Head of Vaccines Research and Development for Novartis Vaccines in Siena, and has most recently pioneered reverse vaccinology, in which the genome of the pathogen is screened for candidate antigenic and immunogenic vaccine components. We spoke to him about the potential for outbreaks of the kind we are now seeing with Ebolavirus in West Africa, and what can be done to prevent them.     

Pitfalls in compressed sensing reconstruction and how to avoid them

Multidimensional NMR can provide unmatched spectral resolution, which is crucial when dealing with samples of biological macromolecules. The resolution, however, comes at the high price of long experimental time. Non-uniform sampling (NUS) of the evolution time domain allows to suppress this limitation by sampling only a small fraction of the data, but requires sophisticated algorithms to reconstruct omitted data points. A significant group of such algorithms known as compressed sensing (CS) is based on the assumption of sparsity of a reconstructed spectrum. Several papers on the application of CS in multidimensional NMR have been published in the last years, and the developed methods have been implemented in most spectral processing software. However, the publications rarely show the cases when NUS reconstruction does not work perfectly or explain how to solve the problem. On the other hand, every-day users of NUS develop their rules-of-thumb, which help to set up the processing in an optimal way, but often without a deeper insight. In this paper, we discuss several sources of problems faced in CS reconstructions: low sampling level, missassumption of spectral sparsity, wrong stopping criterion and attempts to extrapolate the signal too much. As an appendix, we provide MATLAB codes of several CS algorithms used in NMR. We hope that this work will explain the mechanism of NUS reconstructions and help readers to set up acquisition and processing parameters. Also, we believe that it might be helpful for algorithm developers.     

Immunohistochemical mapping of galanin-like neurons in the rat central nervous system

Using an antiserum generated in rabbits against synthetic galanin (GA) and the indirect immunofluorescence method, the distribution of GA-like immunoreactive cell bodies and nerve fibers was studied in the rat central nervous system (CNS) and a detailed stereotaxic atlas of GA-like neurons was prepared. GA-like immunoreactivity was widely distributed in the rat CNS. Appreciable numbers of GA-positive cell bodies were observed in the rostral cingulate and medial prefrontal cortex, the nucleus interstitialis striae terminalis, the caudate, medial preoptic, preoptic periventricular, and preoptic suprachiasmatic nuclei, the medial forebrain bundle, the supraoptic, the hypothalamic periventricular, the paraventricular, the arcuate, dorsomedial, perifornical, thalamic periventricular, anterior dorsal and lateral thalamic nuclei, medial and central amygdaloid nuclei, dorsal and ventral premamillary nuclei, at the base of the hypothalamus, in the central gray matter, the hippocampus, the dorsal and caudoventral raphe nuclei, the interpeduncular nucleus, the locus coeruleus, ventral parabrachial, solitarii and commissuralis nuclei, in the A1, C1 and A4 catechaolamine areas, the posterior area postrema and the trigeminal and dorsal root ganglia. Fibers were generally seen where cell bodies were observed. Very dense fiber bundles were noted in the septohypothalamic tract, the preoptic area, in the hypothalamus, the habenula and the thalamic periventricular nucleus, in the ventral hippocampus, parts of the reticular formation, in the locus coeruleus, the dorsal parabrachial area, the nucleus and tract of the spinal trigeminal area and the substantia gelatinosa, the superficial layers of the spinal cord and the posterior lobe of the pituitary. The localization of the GA-like immunoreactivity in the locus coeruleus suggests a partial coexistence with catecholaminergic neurons as well as a possible involvement of the GA-like peptide in a neuroregulatory role.