The amino-acid mutational spectrum of human genetic disease

Background  

Nonsynonymous mutations in the coding regions of human genes are responsible for phenotypic differences between humans and for susceptibility to genetic disease. Computational methods were recently used to predict deleterious effects of nonsynonymous human mutations and polymorphisms. Here we focus on understanding the amino-acid mutation spectrum of human genetic disease. We compare the disease spectrum to the spectra of mutual amino-acid mutation frequencies, non-disease polymorphisms in human genes, and substitutions fixed between species.     

The toxicity of textile reactive azo dyes after hydrolysis and decolourisation

The toxicity of C.I. Reactive Black 5 and three Procion dyes, as found in textile effluents, was determined using the bioluminescent bacterium Vibrio fischeri. Hydrolysed Reactive Black had a slightly greater toxicity than the parent form (EC(50) 11.4+/-3.68 and 27.5+/-4.01 mg l(-1), respectively). A baffled bioreactor with anaerobic and aerobic compartments was used to decolourise hydrolysed Reactive Black 5 in a synthetic effluent. Decolourisation of hydrolysed Reactive Black resulted in an increased toxicity (EC(50) 0.2+/-0.03 mg l(-1)). Toxicity was not detectable when decolourised Reactive Black 5 was metabolised under aerobic conditions. No genotoxicity was detected after the decolourisation of either the parent or the hydrolysed reactive dyes, either in vitro or in the bioreactor. The toxicity and genotoxicity of decolourised C.I. Acid Orange 7 was due to the production of 1-amino-2-naphthol (EC(50) 0.1+/-0.03 mg l(-1)).     

Understanding mechanisms of novel gene expression in polyploids

Polyploidy has long been recognized as a prominent force shaping the evolution of eukaryotes, especially flowering plants. New phenotypes often arise with polyploid formation and can contribute to the success of polyploids in nature or their selection for use in agriculture. Although the causes of novel variation in polyploids are not well understood, they could involve changes in gene expression through increased variation in dosage-regulated gene expression, altered regulatory interactions, and rapid genetic and epigenetic changes. New research approaches are being used to study these mechanisms and the results should provide a more complete understanding of polyploidy.     

Alternate energy dissipation? Phenolic metabolites and the xanthophyll cycle

The dynamics of phenolic galloylglucoses (di-, tri-, tetra- and penta-galloylglucose), flavonoids (quercitin and quercitin glycosides) and sideroxylonal were compared with that of xanthophyll cycle-dependent energy dissipation during rapid induction of chilling-dependent photo-inhibition. Pre-dawn xanthophyll cycle engagement of seedlings of Eucalyptus nitens transferred from mild nursery conditions to a low temperature controlled environment increased logarithmically during eight days of treatment. Photochemical efficiency and flavonoids decreased after four days of treatment and non-photochemical quenching after two days of treatment. Galloylglucoses and sideroxylonal decreased linearly during treatment. These results demonstrate that rapid changes in foliar phenolic levels are associated with abrupt changes in the plant environment. It is argued that under these growth-chamber conditions, the xanthophyll cycle facilitated dissipation of excess light energy, lessening the requirement for the dissipation of energy or antioxidant activity through phenolic metabolites.     

All-optical histology using ultrashort laser pulses

As a means to automate the three-dimensional histological analysis of brain tissue, we demonstrate the use of femtosecond laser pulses to iteratively cut and image fixed as well as fresh tissue. Cuts are accomplished with 1 to 10 microJ pulses to ablate tissue with micron precision. We show that the permeability, immunoreactivity, and optical clarity of the tissue is retained after pulsed laser cutting. Further, samples from transgenic mice that express fluorescent proteins retained their fluorescence to within microns of the cut surface. Imaging of exogenous or endogenous fluorescent labels down to 100 microm or more below the cut surface is accomplished with 0.1 to 1 nJ pulses and conventional two-photon laser scanning microscopy. In one example, labeled projection neurons within the full extent of a neocortical column were visualized with micron resolution. In a second example, the microvasculature within a block of neocortex was measured and reconstructed with micron resolution.     

Regulation of hyperpolarization-activated HCN channels by cAMP through a gating switch in binding domain symmetry

Recent X-ray structures show that the binding domains of tetrameric ligand-gated channels form either a 4-fold symmetric gating ring or a 2-fold symmetric dimer of dimers. To determine how such structures function to coordinate the binding of multiple ligands during channel activation, we examined the action of cAMP to enhance the opening of the hyperpolarization-activated HCN2 channels, whose cytoplasmic C terminus forms a gating ring in the presence of cAMP. Using tandem dimers and tetramers in which cAMP binding to selected HCN2 subunits was prevented by a point mutation or deletion, we provide the first direct determination of the energetic effects on gating of each of four ligand binding events and demonstrate the importance of the gating ring for cAMP regulation. We suggest that cAMP binding enhances channel opening by promoting assembly of the gating ring from an unliganded state in which the four subunits interact as a 2-fold symmetric dimer of dimers.     

Reconstruction of the three-dimensional NMR spectrum of a protein from a set of plane projections

Three-dimensional protein NMR spectra can be obtained significantly faster than by traditional methods by a projection-reconstruction procedure related to X-ray tomography. First, two orthogonal projections are acquired in quick two-dimensional experiments with the evolution parameters t₁ or t₂ set to zero. These projections define a three-dimensional lattice; all cross-peaks must lie on this lattice but not all lattice points are occupied. A third experiment with t₁ and t₂ incremented simultaneously and in a fixed ratio, generates a projection onto a tilted plane and thus establishes the positions of all the cross-peaks unambiguously. This projection-reconstruction technique has been tested on the 500 MHz three-dimensional HNCO spectrum of ubiquitin.     

Neuron and glia generating progenitors of the mammalian enteric nervous system isolated from foetal and postnatal gut cultures

Cultures of dissociated foetal and postnatal mouse gut gave rise to neurosphere-like bodies, which contained large numbers of mature neurons and glial cells. In addition to differentiated cells, neurosphere-like bodies included proliferating progenitors which, when cultured at clonal densities, gave rise to colonies containing many of the neuronal subtypes and glial cells present in the mammalian enteric nervous system. These progenitors were also capable of colonising wild-type and aganglionic gut in organ culture and had the potential to generate differentiated progeny that localised within the intrinsic ganglionic plexus. Similar progenitors were also derived from the normoganglionic small intestine of mice with colonic aganglionosis. Our findings establish the feasibility of expanding and isolating early progenitors of the enteric nervous system based on their ability to form distinct neurogenic and gliogenic structures in culture. Furthermore, these experiments provide the rationale for the development of novel approaches to the treatment of congenital megacolon (Hirschsprung's disease) based on the colonisation of the aganglionic gut with progenitors derived from normoganglionic bowel segments.