Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site

The Tetrahymena intron is an RNA catalyst, or ribozyme. As part of its self-splicing reaction, this ribozyme catalyzes phosphoryl transfer between guanosine and a substrate RNA strand. Here we report the refined crystal structure of an active Tetrahymena ribozyme in the absence of its RNA substrate at 3.8 A resolution. The 3'-terminal guanosine (omegaG), which serves as the attacking group for RNA cleavage, forms a coplanar base triple with the G264-C311 base pair, and this base triple is sandwiched by three other base triples. In addition, a metal ion is present in the active site, contacting or positioned close to the ribose of the omegaG and five phosphates. All of these phosphates have been shown to be important for catalysis. Therefore, we provide a picture of how the ribozyme active site positions both a catalytic metal ion and the nucleophilic guanosine for catalysis prior to binding its RNA substrate.     

Cloning, characterization and expression of CDK5RAP1_v3 and CDK5RAP1_v4, two novel splice variants of human CDK5RAP1

Two novel splice variants of CDK5RAP1, named CDK5RAP1_v3 and CDK5RAP1_v4, were isolated through the large-scale sequencing analysis of a human fetal brain cDNA library. The CDK5RAP1_v3 and CDK5RAP1_v4 cDNAs are 1923bp and 1792bp in length, respectively. Sequence analysis revealed that CDK5RAP1_v4 lacked 1 exon, which was present in CDK5RAP1_v3, with the result that these cDNAs encoded different putative proteins. The deduced proteins were 574 amino acids (designated as CDK5RAP1_v3) and 426 amino acids (CDK5RAP1_v4) in length, and shared the 420 N-terminal amino acids. RT-PCR analysis showed that human CDK5RAP1_v3 was widely expressed in human tissues. The expression level of CDK5RAP1_v3 was relatively high in placenta and lung, whereas low levels of expression were detected in heart, brain, liver, skeletal muscle, pancreas, spleen, thymus, small intestine and peripheral blood leukocytes. In contrast, human CDK5RAP1_v4 was mainly expressed in brain, placenta and testis.     

The tetrameric L27 domain complex as an organization platform for supramolecular assemblies

L27 domain, initially identified in the Caenorhabditis elegans Lin-2 and Lin-7 proteins, is a protein interaction module that exists in a large family of scaffold proteins. The domain can function as an organization center of large protein assemblies required for establishment and maintenance of cell polarity. We have solved the high-resolution NMR structure of a tetrameric complex of L27 domains containing two SAP97-mLin-2 L27 domain heterodimers. Each L27 domain contains three a-helices. The first two helices of each domain are packed together to form a four-helical bundle in the heterodimer. The third helix of each L27 domain forms another four-helical bundle that assembles the two heterodimers into a tetramer. The structure of the complex provides a mechanistic explanation for L27 domain-mediated polymerization of scaffold proteins, a process that is crucial for the assembly of supramolecular complexes in asymmetric cells.     

Short columns with molecularly imprinted monolithic stationary phases for rapid separation of diastereomers and enantiomers

Three molecularly imprinted monolithic columns with different length but almost identical column volume had been prepared. It was observed that the separation factors of diastereomers and enantiomers were almost unaffected by column length. However, the short column with dimension of 38 mm x 8 mm i.d. showed much lower resistance to flow rate so that it could be operated at much higher flow rates. By combining stepwise gradient elution with elevated flow rate, the diastereomers of cinchonine and cinchonidine and the enantiomers of Cbz-DL-Trp and Fmoc-DL-Trp were successfully separated within 3 min on the short column with dimension of 38 mm x 8 mm i.d. Based on the above results, a cinchonine imprinted monolithic disk with dimension of 10mm x 16 mm i.d. was further developed. The SEM image and the pore size distribution profile showed that large flow-through pores are present on the prepared monolith, which allowed mobile phase to flow through the disk with very low resistance. Chromatographic performances on the monolithic disk were almost unchanged compared with the long columns. A rapid separation of cinchonine and cinchonidine was achieved in 2.5 min at the flow rate of 9.0 ml/min. Furthermore, it was observed that there was almost no effect of the flow rate on the dynamic binding capacity at high flow rates. In addition, the effect of the loading concentration of analytes on the dynamic binding capacity, namely adsorption isotherm, was also investigated. A non-linear adsorption isotherm of cinchonine was observed on the molecularly imprinted monolith with cinchonine as template, which might be a main reason to result in the peak tailing of template molecule.     

Determination of vincristine in mouse plasma and brain tissues by liquid chromatography-electrospray mass spectrometry

Vincristine is an anticancer agent that continues to be examined in preclinical models even though it is used in a variety of human neoplastic disorders. We developed a sensitive liquid chromatography-mass spectrometry (LC-MS) method for the determination of vincristine in plasma and in brain tissues that would support investigations on drug distribution into tissues in animal models. The procedure required only a small sample volume (10 microl) of plasma, which circumvented a limitation of most other assays that were developed for human samples. A solid-phase extraction procedure was employed that enabled the eluent to be directly injected onto a reversed-phase chromatographic HPLC system using positive electrospray ionization followed by mass spectrometric detection. The extraction recoveries of vincristine were 57 and 60% from plasma and brain tissues, respectively. The mobile phase consisted of methanol and 15 mM ammonium acetate in 0.02% formic acid (70:30) that was pumped at 0.2 ml/min to yield retention times of 1.6 and 1.8 min for vincristine and vinblastine, the internal standard, respectively. The method was validated at vincristine plasma concentrations from 0.01 to 2 microg/ml, and from 0.01 to 1 microg/g in brain tissue. The advantage of the method enabled the quantitation of vincristine in multiple plasma samples obtained from a single mouse, which permitted the accurate estimation of its pharmacokinetic properties.     

An analysis of the proteomic profile for Thermoanaerobacter tengcongensis under optimal culture conditions

The genome of Thermoanaerobacter tengcongensis is estimated to encode 2588 theoretical proteins. In this study, we have vitalized approximately 46% of the theoretical proteome experimentally using a proteomic strategy that combines three different methods, shotgun digestion plus high-performance liquid chromatography (HPLC) with ion-trap tandem mass spectrometry (shotgun-liquid chromatography (LC)/MS), one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) plus HPLC with ion-trap tandem mass spectrometry (one-dimensional electrophoresis (1DE)-LC/MS), and two-dimensional gel electrophoresis plus matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (2DE-MALDI-TOF-MS). Of the 1200 proteins identified, as few as 76 proteins were globally found by all three approaches, and notably, most of these proteins were in the soluble fraction. However, there were a number of unique proteins detected by one method only, suggesting that our strategy provides a means toward obtaining a comprehensive view of protein expression profile. Proteins from the major metabolic pathways are strongly represented on the map, and a number of these enzymes were identified by more than one proteomic method. Based upon the proteins identified in the present study, we are able to broaden the understanding of how T. tengcongensis survives under high temperature environment, whereas several of its properties can not be fully explained by genome data.     

Tissue distribution and purification of prophenoloxidase in larvae of Asian Corn Borer, Ostrinia furnacalis Guenee (Lepidoptera: Pyralidae)

Using ammonium sulphate precipitation, Blue-Sepharose CL-6B, Phenyl-Sepharose CL-4B, prophenoloxidase (PPO) was isolated and purified from hemolymph of Ostrinia furnacalis larvae. This zymogen was a heterodimer, and composed of two subunits with the relative molecular mass ranging from 66.2 kD to 97.4 kD determined by SDS-PAGE. Western blotting and indirect immunofluorescence test showed that PPO was present in integument, hemolymph plasma and cell membrane of granular hemocytes and oenocytoids of O. furnacalis larvae.     

An imaging system for standardized quantitative analysis of <Emphasis Type="Italic">C. elegans</Emphasis> behavior

Background  

The nematode Caenorhabditis elegans is widely used for the genetic analysis of neuronal cell biology, development, and behavior. Because traditional methods for evaluating behavioral phenotypes are qualitative and imprecise, there is a need for tools that allow quantitation and standardization of C. elegans behavioral assays.     

Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and cDNA array

Cotton fibers are differentiated epidermal cells originating from the outer integuments of the ovule. To identify genes involved in cotton fiber elongation, we performed subtractive PCR using cDNA prepared from 10 days post anthesis (d.p.a.) wild-type cotton fiber as tester and cDNA from a fuzzless-lintless (fl) mutant as driver. We recovered 280 independent cDNA fragments including most of the previously published cotton fiber-related genes. cDNA macroarrays showed that 172 genes were significantly up-regulated in elongating cotton fibers as confirmed by in situ hybridization in representative cases. Twenty-nine cDNAs, including a putative vacuolar (H⁺)-ATPase catalytic subunit, a kinesin-like calmodulin binding protein, several arabinogalactan proteins and key enzymes involved in long chain fatty acid biosynthesis, accumulated to greater than 50-fold in 10 d.p.a. fiber cells when compared to that in 0 d.p.a. ovules. Various upstream pathways, such as auxin signal transduction, the MAPK pathway and profilin- and expansin-induced cell wall loosening, were also activated during the fast fiber elongation period. This report constitutes the first systematic analysis of genes involved in cotton fiber development. Our results suggest that a concerted mechanism involving multiple cellular pathways is responsible for cotton fiber elongation.