Mapping using unique sequences

Theoretical predictions are given for the progress expected, when mapping DNA by identifying clones containing specific unique sequences. Progress is measured in three ways; however, all results depend on (dimensionless counterparts of) the number of clones and the number of unique sequences used. Furthermore, the effects of clone length dispersion are included in the theoretical predictions. Both the clones in the library and the unique sequences are assumed to be generated randomly, with uniform probability of originating at any base in the region to be mapped. The first measure of progress is the expected length fraction of the region to be mapped covered by at least one clone, when clones containing at least one unique sequence are included in the map. The second measure of progress is the expected length fraction of the region to be mapped in "covered intervals", an interval being the region between adjacent unique sequences. Alternative definitions for clones covering an interval are analyzed. The third measure of progress is the expected number of clone islands generated; an island covers successive intervals. Finally, using these measures of progress, we compare the efficiency of this new mapping strategy with conventional clone mapping strategies.     

A Heuristic-Based Wormhole Routing Algorithm for Hypercube Multicomputer Networks

In this paper, we consider fault-tolerant routing algorithms in hypercube multicomputer networks. In particular, one of the most quoted adaptive fault-tolerant routing algorithm for hypercubes in the literature is studied in detail and its limited ability to route messages in the presence of some fault patterns (i.e., combination of node and link faults), is pointed out. A modified algorithm is proposed and its performance, using simulation, is compared to that of the above mentioned algorithm. It is shown that the proposed algorithm outperforms the existing one in terms of its ability to route routable messages around the hypercube in the presence of node and/or links faults. This improvement is achieved while using the same average path length or even improving it. Illustrative examples are shown in support of such improvement.     

A mathematical model of actin filament turnover for fitting FRAP data

A novel mathematical model of the actin dynamics in living cells under steady-state conditions has been developed for fluorescence recovery after photobleaching (FRAP) experiments. As opposed to other FRAP fitting models, which use the average lifetime of actins in filaments and the actin turnover rate as fitting parameters, our model operates with unbiased actin association/dissociation rate constants and accounts for the filament length. The mathematical formalism is based on a system of stochastic differential equations. The derived equations were validated on synthetic theoretical data generated by a stochastic simulation algorithm adapted for the simulation of FRAP experiments. Consistent with experimental findings, the results of this work showed that (1) fluorescence recovery is a function of the average filament length, (2) the F-actin turnover and the FRAP are accelerated in the presence of actin nucleating proteins, (3) the FRAP curves may exhibit both a linear and non-linear behaviour depending on the parameters of actin polymerisation, and (4) our model resulted in more accurate parameter estimations of actin dynamics as compared with other FRAP fitting models. Additionally, we provide a computational tool that integrates the model and that can be used for interpretation of FRAP data on actin cytoskeleton.     

Pulmonary diffusing capacity in the presence of ventilation inhomogeneity

A model has been developed to quantify the effectiveness of alveolar-capillary transport in the presence of ventilation inhomogeneity. The exhalation dynamics of carbon monoxide (CO), argon (Ar), and lung volume from a single-breath experiment are analyzed simultaneously. A membrane transport coefficient (MTCO) that does not vary with lung volume is evaluated by a two-stage optimization procedure and related to diffusing capacity. Also, the model allows for a decrease in membrane transport rate associated with reduced lung volume. The model is tested by simulation studies and experiments with human subjects having normal or diseased (mainly obstructed) lungs. The MTCO provides a clear distinction between normal and obstructed lungs with respect to alveolar-capillary transport, whereas the semilog slope of the Ar alveolar plateau characterizes the ventilation inhomogeneity. Only when the diffusing capacity is corrected by the Ar slope, DLCO(Ar), do the breathing maneuvers performed from different preinflation volumes (residual volume or functional residual capacity) yield the same results for lungs with ventilation inhomogeneity. The uncorrected DLCO overestimates the effectiveness of alveolar-capillary transport in the presence of ventilation inhomogeneity.     

Diffusion in lung gas and across alveolar membrane in mammalian lungs

The relative importance of stratified inhomogeneity in the mammalian lung has been considered both theoretically and experimentally. Calculations show that alveolar-capillary diffusion resistance is not limiting for inert gas exchange. Previous model calculations have concluded that stratified inhomogeneity is not likely to be an important mechanism in limiting gas exchange. Experimental data with inspired boluses of inert gas show the presence of stratified inhomogeneity. However, another possible mechanism, related to interaction of diffusion and convection, remains as a possible explanation for these findings. Stratified inhomogeneity appears to play a role in gas exchange in the normal rat, but the role of stratified inhomogeneity in humans and other animals is yet to be determined.     

Mathematical modelling of intra- and extracellular potentials generated by active structures with short regions of increased diameter

The Hodgkin-Huxley (1952) model was used to calculate intracellular potentials by the method of Joyner et al. (1978). Extracellular potentials were estimated on the basis of a mathematical model proposed by us. It has shown that, irrespective of practical isopotentiality of the membrane of a local inhomogeneity, the latter affects extracellular potentials in two ways: 1) through changes in the potential profile in the region of the structure before the inhomogeneity; 2) through its own potential profile. The first effect is considerably greater than the second one, but the second is greater than the effect of the equal portion of the thin fibre. Increase in the diameter or length of an inhomogeneity is combined with such changes in the potential profile, that the effect of the inhomogeneity on the extracellular potential amplitude is practically independent of its actual size. The extracellular potential waveform substantially depends on the ratio of the diameters of the two parts of the structure and on the position of the inhomogeneity in relation to the sealed structure end. Registration of the positive-negative potentials having a large positive phase should not be considered as an indication of passive properties of the structure.     

ASEXUAL DEVELOPMENTAL PATTERNS OF THE DIATOM STAURONEIS ANCEPS IN CULTURE123

During several months under controlled growth conditions, cell division in the diatom Stauroneis anceps resulted in a gradual decrease in length as predicted by the Macdonald-Pfitzer hypothesis. Cells of a clone decreased in average length from 35 to 17 μ. The smallest cell observed measured 12 μ. Cells longer than 26 μ typically had capitate ends. As the cells became shorter, there was a gradual decrease in this capitate configuration with the smallest cells being oval in outline. The estimated increment of size reduction due to cell division in the clone was 0.1 μ per division. This value is dependent on the assumption of random division. Populations with cells less than 28 μ in length showed an increase in valve aberrations, but these cells continued to reproduce. A cell 13 μ long and similar to the smallest specimen of the clone was observed from a core sample with fossil specimens of S. anceps.     

A Positive Detecting Code and Its Decoding Algorithm for DNA Library Screening

The study of gene functions requires high-quality DNA libraries. However, a large number of tests and screenings are necessary for compiling such libraries. We describe an algorithm for extracting as much information as possible from pooling experiments for library screening. Collections of clones are called pools, and a pooling experiment is a group test for detecting all positive clones. The probability of positiveness for each clone is estimated according to the outcomes of the pooling experiments. Clones with high chance of positiveness are subjected to confirmatory testing. In this paper, we introduce a new positive clone detecting algorithm, called the Bayesian network pool result decoder (BNPD). The performance of BNPD is compared, by simulation, with that of the Markov chain pool result decoder (MCPD) proposed by Knill et al. in 1996. Moreover, the combinatorial properties of pooling designs suitable for the proposed algorithm are discussed in conjunction with combinatorial designs and dhbox{-}{rm disjunct} matrices. We also show the advantage of utilizing packing designs or BIB designs for the BNPD algorithm.     

Investigation of alginate gel inhomogeneity in simulated gastro-intestinal conditions using magnetic resonance imaging and transmission electron microscopy

The inhomogeneity of alginate gel beads prepared by an external diffusion method has been characterised using spatially resolved nuclear magnetic resonance or “magnetic resonance imaging” (MRI) and transmission electron microscopy (TEM). The beads exhibited various degrees of inhomogeneity although reducing the length of exposure to the gelling bath and the presence of non-gelling ions decreased gel inhomogeneity. In order to gain information regarding the gastro-intestinal functionality of these beads for in vivo applications, they were exposed to simulated gastro-intestinal conditions. The increased polymer concentration at the edge of the beads was shown to persist throughout our gastro-intestinal model despite the centre of the bead becoming progressively more porous in nature. The porosity of the alginate gels has been quantified by image analysis of transmission electron micrographs and shown to depend on both location within the bead and gastro-intestinal conditions. We suggest that such changes in porosity of these alginate beads during simulated gastro-intestinal conditions may make these an attractive option for controlled delivery applications in vivo.     

The Effect of Spatial Inhomogeneity of the Cornea on the Deformation Properties of the Eyeball and the Results of Maklakoff Applanation Tonometry

A two-component model of the eyeball that represents the cornea as a momentless, linearly elastic deformable surface and the scleral region, as an elastic element that responds to intraocular pressure changes by volume changes, has been used to analyze the effect of spatial inhomogeneity in the distribution of effective corneal stiffness on the mechanical properties of the eye. The effective stiffness of the cornea characterized both the elastic properties and the thickness of the cornea within the framework of the model. Various axisymmetric forms of the effective stiffness distribution characterized by monotonic increase along the arc between a point on the corneal surface and the apex of the cornea were studied. The considered distributions simulated both natural inhomogeneity and apical region weakening due to surgical interventions. Numerical simulation yielded the dependences of deformation parameters on intraocular pressure changes. These parameters characterized the deformation properties of both the cornea (apex displacement) and the eyeball as a whole (intraocular volume change). In the case of moderate inhomogeneity, the dependences were only slightly different from those for a homogeneous cornea with an effective stiffness equal to the mean value for the corresponding inhomogeneous distribution. A noticeable increase in the integral response of the cornea and the eyeball as a whole to changes in pressure was observed if the effective stiffness amplitude was very high (two or more times higher than the mean value). The effect of inhomogeneity on the results of tonometric measurements with a Maklakoff tonometer (flat stamp) was studied. The tonometric difference, that is, the difference between the tonometric pressure (in the loaded eye) and the true pressure (before loading), mainly depended on the average stiffness of the cornea in this case as well, with a substantial increase observed at very high stiffness amplitudes only. Apical weakening of the cornea led to an increase (although not very pronounced) of the tonometric difference.     

Robust estimation of multivariate covariance components

In many settings, such as interlaboratory testing, small area estimation in sample surveys, and heritability studies, investigators are interested in estimating covariance components for multivariate measurements. However, the presence of outliers can seriously distort estimates obtained using standard procedures such as maximum likelihood. We propose a procedure based on M-estimation for robustly estimating multivariate covariance components in the presence of outliers; the procedure applies to balanced and unbalanced data. We present an algorithm for computing the robust estimates and examine the performance of the estimator through a simulation study. The estimator is used to find covariance components and identify outliers in a study of variability of egg length and breadth measurements of American coots.     

Efficient characterization of inhomogeneity in contraction strain pattern

Cardiac dyssynchrony often accompanies patients with heart failure (HF) and can lead to an increase in mortality rate. Cardiac resynchronization therapy (CRT) has been shown to provide substantial benefits to the HF population with ventricular dyssynchrony; however, there still exists a group of patients who do not respond to this treatment. In order to better understand patient response to CRT, it is necessary to quantitatively characterize both electrical and mechanical dyssynchrony. The quantification of mechanical dyssynchrony via characterization of contraction strain field inhomogeneity is the focus of this modeling investigation. Raw data from a 3D finite element (FE) model were received from Roy Kerckhoffs et al. and analyzed in MATLAB. The FE model consisted of canine left and right ventricles coupled to a closed circulation with the effects of the pericardium acting as a pressure on the epicardial surface. For each of three simulations (normal synchronous, SYNC, right ventricular apical pacing, RVA, and left ventricular free wall pacing, LVFW) the Gauss point locations and values were used to generate lookup tables (LUTs) with each entry representing a location in the heart. In essence, we employed piecewise cubic interpolation to generate a fine point cloud (LUTs) from a course point cloud (Gauss points). Strain was calculated in the fiber direction and was then displayed in multiple ways to better characterize strain inhomogeneity. By plotting average strain and standard deviation over time, the point of maximum contraction and the point of maximal inhomogeneity were found for each simulation. Strain values were organized into seven strain bins to show operative strain ranges and extent of inhomogeneity throughout the heart wall. In order to visualize strain propagation, magnitude, and inhomogeneity over time, we created 2D area maps displaying strain over the entire cardiac cycle. To visualize spatial strain distribution at the time point of maximum inhomogeneity, a 3D point cloud was created for each simulation, and a CURE index was calculated. We found that both the RVA and LFVW simulations took longer to reach maximum contraction than the SYNC simulation, while also exhibiting larger disparities in strain values during contraction. Strain in the hoop direction was also analyzed and was found to be similar to the fiber strain results. It was found that our method of analyzing contraction strain pattern yielded more detailed spacial and temporal information about fiber strain in the heart over the cardiac cycle than the more conventional CURE index method. We also observed that our method of strain binning aids in visualization of the strain fields, and in particular, the separation of the mass points into separate images associated with each strain bin allows the strain pattern to be explicitly compartmentalized.     

Hybridization-based mapping of Neurospora crassa linkage groups II and V

As part of the German Neurospora crassa genome project, physical clone maps of linkage groups II and V of N. crassa were generated by hybridization-based mapping. To this end, two different types of clone library were used: (1) a bacterial artificial clone library of 15-fold genome coverage and an average insert size of 69 kb, and (2) three cosmid libraries--each cloned in a different vector--with 17-fold coverage and 34 kb average insert size. For analysis, the libraries were arrayed on filters. At the first stage, chromosome-specific sublibraries were selected by hybridization of the respective chromosomal DNA fragments isolated from pulsed-field electrophoresis gels. Subsequently, the sublibraries were exhaustively ordered by single clone hybridizations. Eventually, the global libraries were used again for gap filling. By this means, physical maps were generated that consist of 13 and 21 contigs, respectively, and form the basis of the current sequencing effort on the two chromosomes.     

一种提高水稻FISH检出率的新方法——RFLP混合标记

分别以水稻1号染色体上混合示记的8个紧密连锁的RFLP（平均约1.7kb）和5号染色体的BAC克隆44B4（137kb）,以及12号染色体单个RFLP RG397（约1.5kb）为探针,在水稻染色体上进行了荧光原位杂交（FISH）。结果表明,RFLP混合标记杂交的检出率为27％,大大高于 RFLP的检出率（7％）。其检出率虽然低于BAC克隆44B4（60％）,但它具有程序简单易行的特点,使基因原位定位更加高效,由于水稻中与已知功能基因紧密边销的RFLP标记具有数量丰富、分布密集等优势,揭示了混合标记的RFLP在禾本科植物同线性和共线性分析中的广阔应用前景。此外,混合标记的RFLP带可以用于染色体的准确识别和核型分析。     

Genetic transformation of somatic cells. III. An analysis of the status of the plasmid nucleotide sequences in the extrachromosomal DNA of transformant clone cells and the rescue of extrachromosomal molecules of the plasmid DNA

Extrachromosomal DNAs from TK+ transformant clones of A238 Chinese hamster cells isolated after the treatment with plasmid pST826 containing thymidine kinase gene (TK-gene) of Herpes simplex virus (HSV1) and 1.8 kb insert of human satellite III DNA (HSIII) were studied by hybridization technique. In two TK+-clones (2T301 and 2T16) large quantities of rearranged plasmid DNA molecules were found. Electron microscopy show in clone 2T301 the presence of circular DNAs with average length being 4.64 +/- 0.27 kb. These molecules were rescued by retransformation into E. coli and analysed by restriction mapping and hybridization. All of them contain deletions spanning the entire TK gene of HSV1 and pBR325 sequences situated just downstream from the ORI of replication. The origin of extra-replicating circular DNA in 2T301 clone is discussed.     

指数施肥对楸树无性系生物量分配和根系形态的影响

为探求楸树不同无性系生物量分配和根系形态的差异,2011年3-8月在甘肃省天水市小陇山林科所,以2年生楸树无性系1-4、7080和015-1组培苗为试验材料,设置了CK、6、10、14 g尿素/株4个处理,研究指数施肥对楸树无性系生物量分配和根系形态的影响.结果表明:(1)同一无性系中,10 g尿素/株的根、茎、叶生物量及总生物量、根长、根表面积、根体积和根平均直径均高于其它处理.无性系015-1的生物量和根系形态参数整体上高于无性系1-4和7080.无性系015-1在10 g尿素/株的根、茎、叶生物量及总生物量分别为89.44 g、61.30 g、79.97 g、230.71 g,是CK的1.48、1.52、2.09、1.66倍;根长、根表面积和根体积为22667 cm、6260 cm2、578.14 cm3,是CK的1.94、1.54、2.43倍.(2)指数施肥和无性系的遗传差异明显影响楸树不同无性系生物量的分配格局.适量施氮明显促进3个楸树无性系生物量的积累,而氮素缺乏或过量均不利于生物量的积累.8月同一无性系的根冠比均随施氮量的增加而降低;同一处理下无性系7080的根冠比高于无性系1-4和015-l.无性系1-4和7080的生物量主要向叶和茎分配,而无性系015-1主要向叶分配.(3)指数施肥在6月和7月主要促进细根根长和根表面积的增加;指数施肥在8月主要促进细根、中等根和粗根体积的急剧增加,分别比7月高达36.88％、124.96％、154.79％.这利于根系在中后期吸收更多养分,从而引起生物量分配格局的变化.(4)生物量参数和根系形态参数关系密切.根生物量、地上生物量、总生物量分别和根长、根表面积、根体积、根平均直径极显著正相关;根冠比和根长、根表面积、根体积、根平均直径极显著负相关;比根长和地上生物量、总生物量显著正相关,和根冠比极显著负相关.     

Characterization of the bacterial community associated with the surface and mucus layer of whiting (Merlangius merlangus)

The bacterial community inhabiting the mucus layer and surface of whiting was examined to determine whether the bacteria present are a reflection of the surrounding water or an indigenous bacterial flora is present. The outer mucus, mouth mucus and gut of four whiting harvested from a site in the Irish Sea and the surrounding water were examined by terminal restriction fragment length polymorphism (tRFLP) analysis of the 16S rRNA gene and clone library construction. The water community was the most diverse, with only a small number of shared water-mucus phylotypes present. The bacterial flora associated with the outer mucus layer were more diverse than that of the mouth mucus and gut. All three mucus layers were characterized by the presence of a dominant phylotype, identified as clone wom-1, highly similar to Photobacterium iliopiscarium. In addition to other Photobacterium phylotypes, members of the CFB and Clostridia groups were also detected. Subsequently, whiting from 11 different sites along the east and south coast of Ireland were compared by tRFLP analysis. Strikingly, the mucus layer of whiting at all sites was characterized by the presence and dominance of a TRF corresponding to the clone wom-1 which was virtually absent from the water column.