A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data

We describe a statistical method for the characterization of genomic aberrations in single nucleotide polymorphism microarray data acquired from cancer genomes. Our approach allows us to model the joint effect of polyploidy, normal DNA contamination and intra-tumour heterogeneity within a single unified Bayesian framework. We demonstrate the efficacy of our method on numerous datasets including laboratory generated mixtures of normal-cancer cell lines and real primary tumours.     

Partial characterization of protein kinase-catalyzed phosphorylation of low molecular weight proteins in purified preparations of pigeon heart sarcolemma and sarcoplasmic reticulum

Pigeon heart microsomes contain three minor size protein kinase substrates of minimal molecular weights of 22 000, 15 000, and 11 500, as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. When the microsomes were partially loaded with calcium oxalate and subjected to rate zonal and isopynic centrifugations in sucrose density gradient columns, the 22 000 and the 15 000 dalton proteins settled in the heaviest fraction, which was composed mainly of vesicles of sarcoplasmic reticular membranes; the 11 500 dalton protein was concentrated in the lightest fractions, which consisted chiefly of vesicles of sarcolemmal origin. During incubation of the membrane fractions with Mg[γ-³²P]ATP significant amounts of ³²P were incorporated into all these proteins. Incorporation of ³²P into the 15 000 dalton protein was moderately and ³²P incorporation into the 22 000 dalton protein was markedly enhanced in the presence of exogenous soluble cyclic AMP-dependent protein kinase and cyclic AMP. The phosphorylation of the three proteins was virtually unaffected by CA²⁺ concentrations up to 0.1 mM and by ethyleneglycol-bis(β-aminoethylether)-N,N′-tetraacetic acid in the absence of added Ca²⁺.Phosphorylation of the 22 000 and the 11 500 dalton proteins occurred mainly at serine residues. In the 15 000 dalton protein threonine residues were the main site of endogenous phosphorylation. Nearly equal amounts of [³²P]-phosphate were incorporated into threonine and serine residues of this protein when phosphorylation was supported by exogenous cyclic AMP-dependent protein kinase and cyclic AMP.The 15 000 dalton protein could be removed from its membrane attachment by extraction with an acidic chloroform/methanol mixture. This step opens the way for the purification of this membrane-bound protein kinase substrate.     

Directed mutagenesis of Mycobacterium smegmatis 16S rRNA to reconstruct the in vivo evolution of aminoglycoside resistance in Mycobacterium tuberculosis

Drug resistance in Mycobacterium tuberculosis is a global problem, with major consequences for treatment and public health systems. As the emergence and spread of drug‐resistant tuberculosis epidemics is largely influenced by the impact of the resistance mechanism on bacterial fitness, we wished to investigate whether compensatory evolution occurs in drug‐resistant clinical isolates of M. tuberculosis. By combining information from molecular epidemiology studies of drug‐resistant clinical M. tuberculosis isolates with genetic reconstructions and measurements of aminoglycoside susceptibility and fitness in Mycobacterium smegmatis, we have reconstructed a plausible pathway for how aminoglycoside resistance develops in clinical isolates of M. tuberculosis. Thus, we show by reconstruction experiments that base changes in the highly conserved A‐site of 16S rRNA that: (i) cause aminoglycoside resistance, (ii) confer a high fitness cost and (iii) destabilize a stem‐loop structure, are associated with a particular compensatory point mutation that restores rRNA secondary structure and bacterial fitness, while maintaining to a large extent the drug‐resistant phenotype. The same types of resistance and associated mutations can be found in M. tuberculosis in clinical isolates, suggesting that compensatory evolution contributes to the spread of drug‐resistant tuberculosis disease.     

Underground Vendobionta From Namibia

The late Precambrian fossils from Namibia have generally been regarded as soft-bodied organisms whose three-dimensional preservation resulted from smothering in fluidized sand. The sedimentological context of Pteridinium and Namalia within a sandstone bed, however, allows us to distinguish between two taphocoenoses: (1) winnowed, laterally collapsed, current-transported specimens accumulated as a lag deposit of turbidite-like flows, and (2) specimens 'floating' in the top part of an event bed with their vanes extending upwards to the upper bedding surface. The second taphocoenosis is interpreted as an in situ preserved 'infaunal' community. The immobile underground life habit and the bizarre modes of growth of Pteridinium and Namalia do not fit any extinct or modern group of multicellular organisms. Similar statements can be made for Ernietta and Rangea , thus reviving the Vendobionta hypothesis.     

Seeded Synthesis of CdSe/CdS Rod and Tetrapod Nanocrystals

We demonstrate a method for the synthesis of multicomponent nanostructures consisting of CdS and CdSe with rod and tetrapod morphologies. A seeded synthesis strategy is used in which spherical seeds of CdSe are prepared first using a hot-injection technique. By controlling the crystal structure of the seed to be either wurtzite or zinc-blende, the subsequent hot-injection growth of CdS off of the seed results in either a rod-shaped or tetrapod-shaped nanocrystal, respectively. The phase and morphology of the synthesized nanocrystals are confirmed using X-ray diffraction and transmission electron microscopy, demonstrating that the nanocrystals are phase-pure and have a consistent morphology. The extinction coefficient and quantum yield of the synthesized nanocrystals are calculated using UV-Vis absorption spectroscopy and photoluminescence spectroscopy. The rods and tetrapods exhibit extinction coefficients and quantum yields that are higher than that of the bare seeds. This synthesis demonstrates the precise arrangement of materials that can be achieved at the nanoscale by using a seeded synthetic approach.     

Effects of sensory deprivation on the development of asymmetrical synapses in mouse barrels

Alterations in the numerical density and structure of asymmetrical synapses were examined in thin sections through barrel D4 in six CD/1 mice, including three controls and three sensory deprived animals. Sensory deprivation was effected by once daily trimming of all large mystacial vibrissae on the contralateral side of the snout from P0. The mice were perfuse-fixed at P20, several days following the termination of rapid synaptic growth during barrel development (White et al. , Somatosens Mot Res 14 : 34-55, 1997). Cerebral hemispheres contralateral to the deprived side were osmicated, sectioned at 40 mum and embedded in plastic for thin sectioning. Sterio's ( J Microsc 134 : 127-136, 1984) procedure combined with serial thin section analysis (Braendgaard and Gundersen, J Neurosci Meth 18 : 39-78, 1986), was applied blindly to systematic random samples of neuropil in barrel hollows and septa. No significant difference in the numerical density, estimated total number, or in the proportion of perforated postsynaptic densities was observed. However, a significant decrease in the diameters of asymmetrical postsynaptic densities was observed in hollow (P < 0.05) and septal (P < 0.05) neuropil of deprived animals. These results demonstrate a significant morphological alteration in asymmetrical synapses of a type consistent with a reduction in synaptic activity consequent to sensory deprivation.     

Fabrication of Dense Non-Circular Nanomagnetic Device Arrays Using Self-Limiting Low-Energy Glow-Discharge Processing

We describe a low-energy glow-discharge process using reactive ion etching system that enables non-circular device patterns, such as squares or hexagons, to be formed from a precursor array of uniform circular openings in polymethyl methacrylate, PMMA, defined by electron beam lithography. This technique is of a particular interest for bit-patterned magnetic recording medium fabrication, where close packed square magnetic bits may improve its recording performance. The process and results of generating close packed square patterns by self-limiting low-energy glow-discharge are investigated. Dense magnetic arrays formed by electrochemical deposition of nickel over self-limiting formed molds are demonstrated.