A coalescence approach to gene conversion

In this paper we develop a coalescent model with intralocus gene conversion. Such models are of increasing importance in the analysis of intralocus variability and linkage disequilibrium. We derive the distribution of the waiting time until a gene conversion event occurs in a sample in terms of the distribution of the length of the transferred segment, zeta. We do not assume any specific form of the distribution of zeta. Further, given that a gene conversion event occurs we find the distribution of (sigma, tau), the end points of the transferred segment and derive results on correlations between local trees in positions chi(1) and chi(2). Among other results we show that the correlation between the branch lengths of two local trees in the coalescent with gene conversion (and no recombination) decreases toward a nonzero constant when the distance between chi(1) and chi(2) increases. Finally, we show that a model including both recombination and gene conversion might account for the lack of intralocus associations found in, e.g., Drosophila melanogaster.     

Sprague Dawley rat mutant with tremor, ataxia, tonic immobility episodes, epilepsy and paralysis

A spontaneous neurological mutation was detected in a colony of Sprague Dawley rats. The animals developed a progressive neurological syndrome characterized by tremor (which appeared at the age of 1 month), ataxia (at 4 months), immobility episodes (after 5-6 months), audiogenic seizures and hindlimb paralysis (after 10 months). Cross breeding experiments indicate that this is an autosomal recessive mutation, which we have named taiep subline.     

Modulation of nitrate reductase: some new insights, an unusual case and a potentially important side reaction

The mechanism of the post-translational modulation of nitrate reductase activity (NR, EC 1.6.6.1) is briefly summarized, and it is shown that by this mechanism nitric oxide production through NR is also rapidly modulated. New and partly unexpected details on the modulation mechanism have been obtained by using immunological techniques. The phosphorylation state of NR has been assessed with peptide antibodies raised against the serine phosphorylation motive of spinach NR. By co-immunoprecipitation experiments, 14-3-3 binding to phospho-NR and the function of Mg(2+) in that process has been elucidated. Conflicting data on the role of NR phosphorylation and 14-3-3 binding in controlling NR proteolysis are discussed. A possible role of other NR inactivating proteins is also briefly considered and the regulation of NR of Ricinus communis is described as an interesting special case that differs from the 'normal' mechanism in several important aspects.     

1,2-alpha-l-Fucosynthase: a glycosynthase derived from an inverting alpha-glycosidase with an unusual reaction mechanism

Fucosyloligosaccharides have great therapeutic potential. Here we present a new route for synthesizing a Fucalpha1,2Gal linkage by introducing glycosynthase technology into 1,2-alpha-l-fucosidase. The enzyme adopts a unique reaction mechanism, in which asparagine-423 activated by aspartic acid-766 acts as a base while asparagine-421 fixes both a catalytic water and glutamic acid-566 (an acid) in the proper orientations. Glycosynthase activity of N421G, N423G, and D766G mutants was examined using beta-fucosyl fluoride and lactose, and among them, the D766G mutant most effectively synthesized 2'-fucosyllactose. 1,2-alpha-l-Fucosynthase is the first glycosynthase derived from an inverting alpha-glycosidase and from a glycosidase with an unusual reaction mechanism.     

A new approach to 'megaprimer' polymerase chain reaction mutagenesis without an intermediate gel purification step

Background  

Site-directed mutagenesis is an efficient method to alter the structure and function of genes. Here we report a rapid and efficient megaprimer-based polymerase chain reaction (PCR) mutagenesis strategy that by-passes any intermediate purification of DNA between two rounds of PCR.     

A therapeutic approach and objective test in the treatment of tremor.

Medical treatment of tremor is deceptive. The biochemical disturbance causing its appearance is not known, so that no specific treatment can be applied. Many substances have been proposed for their antitremulant properties, but clinical results must be interpreted with caution as tremor is a labile symptom which is under many influences. The authors have analysed the clinical effect of an interesting antitremulant drug and have reported an original method for measuring tremor.     

A continuum approach to blood vessel growth: Axisymmetric elastic structures

In this paper we discuss the morphogenesis of small blood vessels (venules) as the nautral consequence of physical forces prevailing during endothelial cell division. A physical model is developed in which the blood vessel is treated as a growing, thin elastic shell embedded in a viscous fluid (i.e. the surrounding tissue). It is explained how a pre-existing cylindrical vessel, induced to grow by some promoter, can buckle and thereby develop a spatially periodic structure displaying varicosity, sinuosity, and/or helicity. Growth manifests itself dynamically in terms of a “growth pressure” which disturbs any pre-existing force balance. The governing set of non-linear partial differential equations are derived, and solutions corresponding to uniform dilation are obtained. The buckled structure emerges as an instability of this time dependent basic state of uniform dilation. A linear stability analysis yields the dominant wavelength of the varicose mode; these results compare favorably with crude measurements made from the experimental literature. In the hope of uncovering the mechanism which underlies the selection of sprouting sites along a parent vessel, it is suggested that reaction and diffusion processes (between growth promoting and inhibiting substances) on buckled surfaces be coupled to the dynamical force balances discussed here.     

A coalescent approach to the polymerase chain reaction.

A versatile algorithm is developed to model PCR on a computer. The method is based on a modification of the coalescent process and provides a general framework to analyse data from PCR. It allows for incorporation of the dynamics of the replication process as described in terms of the number of starting template molecules and cycle-dependent PCR efficiency. The simulation method generates, as a first step, the genealogy of a set of sequences sampled from a final PCR product. In a second step a mutation process is superimposed and the resulting data set is analysed. The efficiency of our algorithm enables us to get reliable approximations of various sample distributions. We demonstrate the relevance of our method with two applications: maximum likelihood estimation of the error rate in PCR and a test of homogeneity of the template.     

Three-dimensional numerical approach to investigate the substrate transport and conversion in an immobilized enzyme reactor

This numerical study evaluates the momentum and mass transfer in an immobilized enzyme reactor. The simulation is based on the solution of the three-dimensional Navier-Stokes equation and a scalar transport equation with a sink term for the transport and the conversion of substrate to product. The reactor consists of a container filled with 20 spherical enzyme carriers. Each of these carriers is covered with an active enzyme layer where the conversion takes place. To account for the biochemical activity, the sink term in the scalar transport equation is represented by a standard Michaelis-Menten approach. The simulation gives detailed information of the local substrate and product concentrations with respect to external and internal transport limitations. A major focus is set on the influence of the substrate transport velocity on the catalytic process. For reactor performance analysis the overall and the local transport processes are described by a complete set of dimensionless variables. The interaction between substrate concentration, velocity, and efficiency of the process can be studied with the help of these variables. The effect of different substrate inflow concentrations on the process can be seen in relation to velocity variations. The flow field characterization of the system makes it possible to understand fluid mechanical properties and its importance to transport processes. The distribution of fluid motion through the void volume has different properties in different parts of the reactor. This phenomenon has strong effects on the arrangement of significantly different mass transport areas as well as on process effectiveness. With the given data it is also possible to detect zones of high, low, and latent enzymatic activity and to determine whether the conversion is limited due to mass transfer or reaction resistances.     

Trisomy 10p, due to an unusual translocation

A mentally retarded boy with short stature, craniofacial dysmorphia, clubfeet, hypertonia and several other congenital anomalies is described. Chromosome analysis revealed a trisomy 10p, due to a peculiar t(10 ; 14) (p11 ; p12) translocation.     

Laughing,Smiling, and Talking: Relation to Sleeping and Social Context in Humans

The propabilities of laughing, smiling, or talking during a given hour and in various social environments were investigated by having undergraduate college students record their performance of these activitics in a log book during a one-week period. All three activities were least likely to occur during the hours immediately before bedtime and after waking and were most frequent in social situations. Smiles and laughs, like talking, were performed primarily during social encounters and were often part of verbal and nonverbal conversations. Because laughing and smiling are phasic social acts, they are of limited value as indices of ongoing (tonic) emotional state. The role of laughing, smiling, and talking in communication, the production of mood, and social bonding is considered.     

A polymer-supported [1,3,2]oxazaphospholidine for the conversion of isothiocyanates to isocyanides and their subsequent use in an ugi reaction

The design and synthesis of a new polymer supported reagent for the clean conversion of isothiocyanates to isocyanides under microwave conditions was accomplished. The structurally diverse isocyanides generated were used in an Ugi 3CC, allowing the rapid generation of 2-isoindolinone-7-carboxamide analogues.