Elastic volume reconstruction from series of ultra-thin microscopy sections

Anatomy of large biological specimens is often reconstructed from serially sectioned volumes imaged by high-resolution microscopy. We developed a method to reassemble a continuous volume from such large section series that explicitly minimizes artificial deformation by applying a global elastic constraint. We demonstrate our method on a series of transmission electron microscopy sections covering the entire 558-cell Caenorhabditis elegans embryo and a segment of the Drosophila melanogaster larval ventral nerve cord.     

Current challenges in open-source bioimage informatics

We discuss the advantages and challenges of the open-source strategy in biological image analysis and argue that its full impact will not be realized without better support and recognition of software engineers' contributions to the biological sciences and more support of this development model from funders and institutions.     

Water-soluble titanocene complexes with sulfur-containing aminoacids: synthesis, spectroscopic, electrochemical and Ti(IV)–transferrin interaction studies

Three new water soluble titanocene–aminoacid complexes have been synthesized via the reaction of Cp₂TiCl₂ and two equivalents of aminoacid (L) in methanol, affording [Cp₂TiL₂]Cl₂, L=L-cysteine (2), D-penicillamine (3) and L-methionine (4). These complexes have been characterized by ¹H, IR and UV-Vis spectroscopies, elemental analysis and cyclic voltammetry. Kinetic studies of ligand hydrolysis have been monitored at low pH using UV-Vis and ¹H NMR spectroscopies to assess their stability in aqueous solution. At low pH, aminoacid ligands are lost one order of magnitude faster than cyclopentadienyl. However, at physiological pH, in Tris buffer solution, the complexes decompose rapidly to form an insoluble titanium compound. The affinity of these complexes to apo-transferrin was also investigated to elucidate how the ancillary aminoacid ligands affect the titanium intake by apo-transferrin.Electronic Supplementary Material Supplementary material is available for this article at     

Multiple Consecutive Infections Might Explain the Lack of Protection by BCG

Although contacts between tuberculosis patients may result in multiple consecutive infections (MCI), no experimental animal models consider this fact when used in basic studies. Moreover, the current TB vaccine (BCG) has demonstrated a limited protection in humans. In this study we evaluate the effect of tuberculosis MCI by way of a simple mathematical analysis using data from the low dose aerosol murine experimental model. The results show that a higher number of, or shorter intervals between, multiple consecutive infections reduce the protective effect of BCG. This is due to both the increase in bacillary load at the stationary level of the infection, and the protective immune response induced by the infection itself. This factor must therefore be taken into account when designing new prophylactic strategies as candidate vaccines for the replacement of BCG.     

The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations

Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroup variation among the elderly and rural populations was significantly greater. Skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~5x greater than random.     

The interplay o light and heat in bleaching rhodopsin

Rhodopsin, the pigment of the retinal rods, can be bleached either by light or by high temperature. Earlier work had shown that when white light is used the bleaching rate does not depend on temperature, and so must be independent of the internal energy of the molecule. On the other hand thermal bleaching in the dark has a high temperature dependence from which one can calculate that the reaction has an apparent activation energy of 44 kg. cal. per mole. It has now been shown that the bleaching rate of rhodopsin becomes temperature-dependent in red light, indicating that light and heat cooperate in activating the molecule. Apparently thermal energy is needed for bleaching at long wave lengths where the quanta are not sufficiently energy-rich to bring about bleaching by themselves. The temperature dependence appears at 590 mµ. This is the longest wave length at which bleaching by light proceeds without thermal activation, and corresponds to a quantum energy of 48.5 kg. cal. per mole. This value of the minimum energy to bleach rhodopsin by light alone is in agreement with the activation energy of thermal bleaching in the dark. At wave lengths between 590 and 750 mµ, the longest wave length at which the bleaching rate was fast enough to study, the sum of the quantum energy and of the activation energy calculated from the temperature coefficients remains between 44 and 48.5 kg. cal. This result shows that in red light the energy deficit of the quanta can be made up by a contribution of thermal energy from the internal degrees of freedom of the rhodopsin molecule. The absorption spectrum of rhodopsin, which is not markedly temperature-dependent at shorter wave lengths, also becomes temperature-dependent in red light of wave lengths longer than about 570 to 590 mµ. The temperature dependence of the bleaching rate is at least partly accounted for by the temperature coefficient of absorption. There is some evidence that the temperature coefficient of bleaching is somewhat greater than the temperature coefficient of absorption at wave lengths longer than 590 mmicro;. This means that the thermal energy of the molecule is a more critical factor in bleaching than in absorption. It shows that some of the molecules which absorb energy-deficient quanta of red light are unable to supply the thermal component of the activation energy needed for bleaching, so bringing about a fall in the quantum efficiency. The experiments show that there is a gradual transition between the activation of rhodopsin by light and the activation by internal energy. It is suggested that energy can move freely between the prosthetic group and the protein moiety of the molecule. In this way a part of the large amount of energy in the internal degrees of freedom of rhodopsin could become available to assist in thermal activation. Assuming that the minimum energy required for bleaching is 48.5 kg. cal., an equation familiar in the study of unimolecular reaction has been used to estimate the number of internal degrees of freedom, n, involved in supplying the thermal component of the activation energy when rhodopsin is bleached in red light. It was found that n increases from 2 at 590 mµ to a minimum value of 15 at 750 mµ. One wonders what value n has at 1050 mµ, where vision still persists, and where rhodopsin molecules may supply some 16 kg. cal. of thermal energy per mole in order to make up for the energy deficit of the quanta.