Antisense probes containing 2-aminoadenosine allow efficient depletion of U5 snRNP from HeLa splicing extracts.

RNA duplexes containing the modified base 2-amino-adenine in place of adenine are stabilized through the formation of three hydrogen bonds in 2-amino A.U base pairs. Antisense 2'-O-alkyloligoribonucleotide probes incorporating 2-aminoadenosine are thus able to efficiently affinity select RNP particles which are otherwise inaccessible. This has allowed the efficient and specific depletion of U5 snRNP from HeLa cell nuclear splicing extracts. U5 snRNP is shown to be essential for spliceosome assembly and for both steps of pre-mRNA splicing. The absence of U5 snRNP prevents the stable association of U4/U6 but not U1 and U2 snRNPs with pre-mRNA.     

Dual expression and anatomy lines allow simultaneous visualization of gene expression and anatomy

Studying the developmental genetics of plant organs requires following gene expression in specific tissues. To facilitate this, we have developed dual expression anatomy lines, which incorporate a red plasma membrane marker alongside a fluorescent reporter for a gene of interest in the same vector. Here, we adapted the GreenGate cloning vectors to create two destination vectors showing strong marking of cell membranes in either the whole root or specifically in the lateral roots. This system can also be used in both embryos and whole seedlings. As proof of concept, we follow both gene expression and anatomy in Arabidopsis (Arabidopsis thaliana) during lateral root organogenesis for a period of over 24 h. Coupled with the development of a flow cell and perfusion system, we follow changes in activity of the DII auxin sensor following application of auxin.

A vector system and flow cell set-up allow long-term imaging of both gene expression and anatomy in Arabidopsis primary and lateral roots.     

Charge engineering of a protein domain to allow efficient ion-exchange recovery

We have created protein domains with extreme surface charge. These mutated domains allow for ion-exchange chromatography under conditions favourable for selective and efficient capture, using Escherichia coli as a host organism. The staphylococcal protein A-derived domain Z (Zwt) was used as a scaffold when constructing two mutants, Zbasic1 and Zbasic2, with high positive surface charge. Far-ultraviolet circular dichroism measurements showed that they have a secondary structure content comparable to the parental molecule Zwt. Although melting temperatures (Tm) of the engineered domains were lower than that of the wild-type Z domain, both mutants could be produced successfully as intracellular full-length products in E. coli and purified to homogeneity by ion-exchange chromatography. Further studies performed on Zbasic1 and Zbasic2 showed that they were able to bind to a cation exchanger even at pH values in the 9 to 11 range. A gene fusion between Zbasic2 and the acidic human serum albumin binding domain (ABD), derived from streptococcal protein G, was also constructed. The gene product Zbasic2-ABD could be purified using cation-exchange chromatography from a whole cell lysate to more than 90% purity.     

Commercial detection methods for biotinylated gene probes: Comparison with32P-labeled DNA probes

This study had two objectives: (a) to determine whether biotinylated DNA probes could be substituted for³²P-labeled DNA probes to detect the presence of the TEM-1 -lactamase gene in crude bacterial preparations, and (b) to evaluate two commercial detection systems for biotinylated probes—an alkaline phosphatase kit produced by Bethesda Research Laboratories (BRL) and an acid phosphatase kit produced by Enzo Biochem. Both the kits produced nonspecific reactions with TEM-1-negative organisms. Treatment with chloroformphenol and proteinase K did not remove these nonspecific reactions. When plasmid DNA was purified by electrophoresis and transferred to nitrocellulose filters by the Southern blot method, there was no qualitative difference between the biotinylated and radioactive probes. However, the³²P-labeled probes were quantitatively 100 times more sensitive than the biotinylated probes. In addition, the Enzo Biochem kit and the³²P-labeled probes could be used with charged nylon membranes, whereas the BRL kit could be used only with nitrocellulose filters.     

Fast track in vitro mycorrhization of potato plantlets allow studies on gene expression dynamics

Root colonization by arbuscular mycorrhizal (AM) fungi is a dynamic process involving major changes in plant gene expression. Here, the expression of a phosphate transporter gene (PT3) and several defense genes, already known to be involved in the various stages of AM establishment, were monitored in the mycelium donor plant (MDP) in vitro culture system associating potato plantlets with an AM fungus. This system allows fast and homogenous mycorrhization of seedlings at their early stage of development by growing the plantlets in active mycelial networks, but has never been validated for gene expression analysis. Here, QRT-PCR analyses were conducted in parallel to pre- (1 day), early (2 and 3 days), and late (6, 9, and 15 days) stages of root colonization. We observed the induction of a plant gene marker of AM root colonization (PT3) at the late stage and the induction of MAPK and PAL genes at the early and late stages of root colonization. We also demonstrated the induction of PR1 and PR2 genes at pre- and late stages and of GST1 and Lox genes at a late stage of root colonization. These results validated the MDP in vitro culture system as an optimal tool to study gene expression analysis during the AM fungi establishment. This system further opened the door to investigate gene networks associated with the plants–AM fungi symbiosis.     

逆转录病毒表达系统及其在外源蛋白高效表达中的应用

逆转录病毒表达系统是一种新的重组蛋白高效表达系统,它由逆转录病毒载体,包膜蛋白载体和包装细胞系构成,在基因治疗和生物制药领域都有很大的应用潜力。逆转录病毒和宿主细胞基因组的重组倾向于发生在转录活性区;口炎疱疹病毒-G蛋白 (vesicular stomatitis virus G, VSV-G)能有效扩大逆转录病毒感染宿主细胞的范围、提高逆转录病毒的感染效率;用高滴度的重组病毒感染细胞,经过简单的筛选即可获得高表达细胞株。本文对逆转录病毒表达系统的组成、感染的特点和机制及其应用前景作了概述。     

Cancer outlier differential gene expression detection

We study statistical methods to detect cancer genes that are over- or down-expressed in some but not all samples in a disease group. This has proven useful in cancer studies where oncogenes are activated only in a small subset of samples. We propose the outlier robust t-statistic (ORT), which is intuitively motivated from the t-statistic, the most commonly used differential gene expression detection method. Using real and simulation studies, we compare the ORT to the recently proposed cancer outlier profile analysis (Tomlins and others, 2005) and the outlier sum statistic of Tibshirani and Hastie (2006). The proposed method often has more detection power and smaller false discovery rates. Supplementary information can be found at http://www.biostat.umn.edu/~baolin/research/ort.html.     

How can conserved gene expression allow for variation? Lessons from the dorso-ventral patterning gene muscle segment homeobox

Arthropods are common in marine, freshwater, terrestrial, and even aerial environments. The arthropod nervous systems must be adjusted to the highly diverse behaviour and requirements of the individual arthropod species. This raises the question of how the underlying patterning mechanisms have changed during arthropod evolution to produce the characteristic axonal scaffold on the one hand and allow for variations in neuronal networks on the other hand. Here we show that the overall number of the neural precursor groups/neuroblasts as well as their spatial arrangement in rows and columns is similar in all four arthropod groups indicating a common origin of this pattern. Furthermore, we demonstrate differences in the expression pattern of the columnar gene muscle segment homeobox and both differences in the expression and regulation of the neural subtype specific genes even-skipped and islet. This variation may underlie the evolutionary variations in neural identity in the individual arthropod groups. Furthermore, we discuss to what extent the stereotyped pattern of neural precursors is required for the conserved axonal scaffold and thus might have been constrained along with the underlying patterning mechanisms.     

High density of octaarginine stimulates macropinocytosis leading to efficient intracellular trafficking for gene expression

The mechanism of the arginine-rich peptide-mediated cellular uptake is currently a controversial issue. Several factors, including the type of peptide, the nature of the cargo, and the linker between them, appear to affect uptake. One of the less studied factors, which may affect the uptake mechanism, is the effect of peptide density on the surface of the cargo. Here, we examined the mechanism of cellular uptake and intracellular trafficking of liposomes modified with different densities of the octaarginine (R8) peptide. Liposomes modified with a low R8 density were taken up mainly through clathrin-mediated endocytosis, leading to extensive lysosomal degradation, whereas those modified with a high R8 density were taken up mainly through macropinocytosis and were less subject to lysosomal degradation. Furthermore, the high density R8-liposomes were able to stimulate the macropinocytosis-mediated uptake of other particles. When plasmid DNA was condensed and encapsulated in R8-liposomes, the levels of gene expression were three orders of magnitude higher for the high density liposomes. The enhanced gene expression by the high density R8-liposomes was highly impaired by blocking uptake through macropinocytosis. The different extents of gene expression from different densities of the R8 peptide on the liposomes could be explained principally by the existence of an intracellular trafficking route, but not by the uptake amount, of internalized liposomes. These results show that the density of the R8 peptide on liposomes determines the uptake mechanism and that this is directly linked to intracellular trafficking, resulting in different levels of gene expression.     

Design of long oligonucleotide probes for functional gene detection in a microbial community

MOTIVATION: Analysis of the functions of microorganisms and their dynamics in the environment is essential for understanding microbial ecology. For analysis of highly similar sequences of a functional gene family using microarrays, the previous long oligonucleotide probe design strategies have not been useful in generating probes. RESULTS: We developed a Hierarchical Probe Design (HPD) program that designs both sequence-specific probes and hierarchical cluster-specific probes from sequences of a conserved functional gene based on the clustering tree of the genes, specifically for analyses of functional gene diversity in environmental samples. HPD was tested on datasets for the nirS and pmoA genes. Our results showed that HPD generated more sequence-specific probes than several popular oligonucleotide design programs. With a combination of sequence-specific and cluster-specific probes, HPD generated a probe set covering all the sequences of each test set. AVAILABILITY: http://brcapp.kribb.re.kr/HPD/