Algorithms for sequence analysis via mutagenesis

Despite many successes of conventional DNA sequencing methods, some DNAs remain difficult or impossible to sequence. Unsequenceable regions occur in the genomes of many biologically important organisms, including the human genome. Such regions range in length from tens to millions of bases, and may contain valuable information such as the sequences of important genes. The authors have recently developed a technique that renders a wide range of problematic DNAs amenable to sequencing. The technique is known as sequence analysis via mutagenesis (SAM). This paper presents a number of algorithms for analysing and interpreting data generated by this technique.

Are there functional P2X receptors on cell bodies in intact dorsal root ganglia of rats?

P2X purinoceptors have been suggested to participate in transduction of painful stimuli in nociceptive neurons. In the current experiments, ATP (1-10 mM), alpha,beta-methylene-ATP (10-30 mu M) and capsaicin (10 nM-1 mu M) were applied to neurons impaled with high resistance microelectrodes in rat dorsal root ganglia (L4 and L5) isolated in vitro together with the sciatic nerve and dorsal roots. The agonists were either bath applied or focally applied using a picospritzer. GABA (100 mu M) and 40-80 mM K+ solutions gave brisk responses when applied by either technique. Only three of 22 neurons with slowly conducting axons (C cells) showed evidence of P2X-purinoceptor-mediated responses. Only two of 13 cells which responded to capsaicin (putative nociceptors), and none of 29 cells with rapidly conducting axons (A cells), responded to the purinergic agonists. When acutely dissociated dorsal root ganglion cells were studied using patch-clamp techniques, all but four of 30 cells of all sizes responded with an inward current to either ATP or alpha,beta-methylene-ATP (both 100 mu M). Our data suggest that few sensory cell bodies in intact dorsal root ganglia express functional purinoceptors. (C) 1998 IBRO. Published by Elsevier Science Ltd.

A pilot study of the manual force levels required to produce manipulation induced hypoalgesia

Objective. A pilot investigation of the influence of different force levels on a treatment technique's hypoalgesic effect. Design. Randomised single blind repeated measures. Background. Optimisation of such biomechanical treatment variables as the point of force application, direction of force application and the level of applied manual force is classically regarded as the basis of best practice manipulative therapy. Manipulative therapy is frequently used to alleviate pain, a treatment effect that is often studied directly in the neurophysiological, paradigm and seldom in biomechanical research. The relationship between the level of force applied by a technique (e.g. biomechanics) and its hypoalgesic effect was the focus of this study. Method. The experiment involved the application of a lateral glide mobilisation with movement treatment technique to the symptomatic elbow of six subjects with lateral epicondylalgia. Four different levels of force, which were measured with a flexible pressure-sensing mat, were randomly applied while the subject performed a pain free grip strength test. Results. Standardised manual force data varied from 0.76 to 4.54 N/cm, lower-upper limits 95 Cl, respectively. Pain free grip strength expressed as a percentage change from pre-treatment values was significantly greater with manual forces beyond 1.9 N/cm (P = 0.014). Conclusions. This study, albeit a pilot, provides preliminary evidence that in terms of the hypoalgesic effect of a mobilisation with movement treatment technique, there may be an optimal level of applied manual force.

Birth of Koalas Phascolarctos cinereus at Lone Pine Koala Sanctuary following artificial insemination

This paper documents the successful development of an artificial insemination (AI) programme for the Koala Phascolurctos cinereus. The protocols for trials involving two methods to induce ovulation and two insemination techniques are described. In Trial 1, interrupted coitus using a 'teaser'♂ successfully induced ovulation in nine Koalas. Five ♀♀ were inseminated while conscious using a modified 'foley catheter' (Cook insemination catheter) resulting in the births of two offspring. The other four ♀♀ were anaesthetized and inseminated using a technique which allowed visualization of the most cranial portion of the urogenital sinus, where semen was deposited using a 3.5 Fr. 'Tom-cat catheter' (urogen-itoscopic insemination). Three of the four ♀♀ inseminated by this technique produced pouch young. Microsatellite analysis of DNA from the pouch young excluded the teaser ♀♀ as possible sires, confirming that all offspring were sired by donor sperm. In Trial 2, eight ♀♀ were induced to ovulate by injecting them with 250 International Units of human chorionic gonadotrophin (hCG). A luteal phase was confirmed in all eight ♀♀ but only one gave birth following urogenitoscopic insemination. The Koala pouch young in this study are the first of any marsupial to be conceived and born following A1 procedures. Details of the A1 procedures used are presented and the significance of A1 to the conservation biology of P. cinereus discussed.

Isolation and characterization of integron-containing bacteria without antibiotic selection

The emergence of antibiotic resistance among pathogenic and commensal bacteria has become a serious problem worldwide. The use and overuse of antibiotics in a number of settings are contributing to the development of antibiotic-resistant microorganisms. The class 1 and 2 integrase genes (intI1 and intI2, respectively) were identified in mixed bacterial cultures enriched from bovine feces by growth in buffered peptone water (BPW) followed by integrase-specific PCR. Integrase-positive bacterial colonies from the enrichment cultures were then isolated by using hydrophobic grid membrane filters and integrase-specific gene probes. Bacterial clones isolated by this technique were then confirmed to carry integrons by further testing by PCR and DNA sequencing. Integron-associated antibiotic resistance genes were detected in bacteria such as Escherichia coli, Aeromonas spp., Proteus spp., Morganella morganii, Shewanella spp., and urea-positive Providencia stuartii isolates from bovine fecal samples without the use of selective enrichment media containing antibiotics. Streptomycin and trimethoprim resistance were commonly associated with integrons. The advantages conferred by this methodology are that a wide variety of integron-containing bacteria may be simultaneously cultured in BPW enrichments and culture biases due to antibiotic selection can be avoided. Rapid and efficient identification, isolation, and characterization of antibiotic resistance-associated integrons are possible by this protocol. These methods will facilitate greater understanding of the factors that contribute to the presence and transfer of integron-associated antibiotic resistance genes in bacterial isolates from red meat production animals.

Determination of a misfit dislocation complex in SiGe/Si heterostructures by image deconvolution technique in HREM

The core structure of a dislocation complex in SiGe/Si system composed of a perfect 60degrees dislocation and an extended 60 dislocation has been revealed at atomic level. This is attained by applying the image deconvolution technique in combination with dynamical diffraction effect correction to an image taken with a 200 kV field-emission high-resolution electron microscope. The possible configuration of the dislocation complex is analyzed and their Burgers vectors are determined. (C) 2003 Elsevier B.V. All rights reserved.

Microstructure of MmM(5)/Mg multi-layer hydrogen storage films prepared by magnetron sputtering

Multi-layer hydrogen storage thin films with Mg and MmNi(3.5)(CoAlMn)(1.5) (here Mm denotes La-rich mischmetal) as alternative layers were prepared by direct current magnetron sputtering. Transmission electron microscopy investigation shows that the microstructure of the MmNi(3.5)(CoAlMn)(1.5) and Mg layers are significantly different although their deposition conditions are the same. The MmNi(3.5)(CoAlMn)(1.5) layer is composed of two regions: one is an amorphous region approximately 4 nm thick at the bottom of the layer and the other is a nanocrystalline region on top of the amorphous region. The Mg layer is also composed of two regions: one is a randomly orientated nanocrystalline region 50 nm thick at the bottom of the layer and the other is a columnar crystallite region on top of the nanocrystalline region. These Mg columnar crystallites have their [001] directions parallel to the growth direction and the average lateral size of these columnar crystallites is about 100 nm. A growth mechanism of the multi-layer thin films is discussed based on the experiment results. Wiley-Liss, Inc.

Comparing the concentration of calcium hydroxide in the diffuse double layer by modeling and experiment

The leaching of elements from the surface of charged fly ash particles is known to be an unsteady process. The mass transfer resistance provided by the diffuse double layer has been quantified as one of the reasons for this delayed leaching. In this work, a model based on mass transfer principles for predicting the concentration of calcium hydroxide in the diffuse double layer is presented. The significant difference between predicted calcium hydroxide concentration and the experimentally measured is explained.

Control of hypersonic turbulent skin friction by boundary-layer combustion of hydrogen

Shvab-Zeldovich coupling of flow variables has been used to extend Van Driest's theory of turbulent boundary-layer skin friction to include injection and combustion of hydrogen in the boundary layer. The resulting theory is used to make predictions of skin friction and heat transfer that are found to be consistent with experimental and numerical results. Using the theory to extrapolate to larger downstream distances at the same experimental conditions, it is found that the reduction in skin-friction drag with hydrogen mixing and combustion is three times that with mixing alone. In application to flow on a flat plate at mainstream velocities of 2, 4, and 6 knits, and Reynolds numbers from 3 X 10(6) to 1 x 10(8), injection and combustion of hydrogen yielded values of skin-friction drag that were less than one-half of the no-injection skin-friction drag, together with a net reduction in heat transfer when the combustion heat release in air was less than the stagnation enthalpy. The mass efficiency of hydrogen injection, as measured by effective specific impulse values, was approximately 2000 s.

Microstructure of MmM(5)/Mg multi-layer films prepared by magnetron sputtering

Microstructure of MmNi(3.5)(CoAlMn)(1.5)/Mg (here Mm denotes La-rich mischmetal) multi-layer hydrogen storage thin films prepared by direct current magnetron sputtering was investigated by cross-sectional transmission electron microscopy (XTEM). It was shown that the MMM5 layers are composed of two regions: an amorphous region with a thickness of similar to 4nm at the bottom of the layers and a randomly orientated nanocrystallite region on the top of the amorphous region and the Mg layers consist of typical columnar crystallite with their [001] direction nearly parallel to the growth direction. The mechanism for the formation of the above microstructure characteristics in the multi-layer thin films has been proposed. Based on the microstructure feature of the multi-layer films, mechanism for the apparent improvement of hydrogen absorption/desorption kinetics was discussed. (c) 2005 Elsevier B.V. All rights reserved.

A blank slate? Layer-by-layer deposition of hyaluronic acid and chitosan onto various surfaces

Although poly(alpha-hydroxy esters), especially the PLGA family of lactic acid/glycolic acid copolymers, have many properties which make them promising materials for tissue engineering, the inherent chemistry of surfaces made from these particular polymers is problematic. In vivo, they promote a strong foreign-body response as a result of nonspecific adsorption and denaturation of serum proteins, which generally results in the formation of a nonfunctional fibrous capsule. Surface modification post-production of the scaffolds is an often-utilized approach to solving this problem, conceptually allowing the formation of a scaffold with mechanical properties defined by the bulk material and molecular-level interactions defined by the modified surface properties. A promising concept is the so-called blank slate: essentially a surface that is rendered resistant to nonspecific protein adsorption but can be readily activated to covalently bind bio-functional molecules such as extracellular matrix proteins, growth factors or polysaccharides. This study focuses on the use of the quartz crystal microbalance (QCM) to follow the layer-by-layer (LbL) electrostatic deposition of high molecular weight hyaluronic acid and chitosan onto PLGA surfaces rendered positively charged by aminolysis, to form a robust, protein-resistant coating. We further show that this surface may be further functionalized via the covalent attachment of collagen IV, which may then be used as a template for the self-assembly of basement membrane components from dilute Matrigel. The response of NIH-3T3 fibroblasts to these surfaces was also followed and shown to closely parallel the results observed in the QCM.

Interpretation of negative values of the interaction parameter in the adsorption equation through the effects of surface layer heterogeneity

The problem of the negative values of the interaction parameter in the equation of Frumkin has been analyzed with respect to the adsorption of nonionic molecules on energetically homogeneous surface. For this purpose, the adsorption states of a homologue series of ethoxylated nonionic surfactants on air/water interface have been determined using four different models and literature data (surface tension isotherms). The results obtained with the Frumkin adsorption isotherm imply repulsion between the adsorbed species (corresponding to negative values of the interaction parameter), while the classical lattice theory for energetically homogeneous surface (e.g., water/air) admits attraction alone. It appears that this serious contradiction can be overcome by assuming heterogeneity in the adsorption layer, that is, effects of partial condensation (formation of aggregates) on the surface. Such a phenomenon is suggested in the Fainerman-Lucassen-Reynders-Miller (FLM) 'Aggregation model'. Despite the limitations of the latter model (e.g., monodispersity of the aggregates), we have been able to estimate the sign and the order of magnitude of Frumkin's interaction parameter and the range of the aggregation numbers of the surface species. (C) 2004 Elsevier B.V All rights reserved.