Biomedical subjects

Ligang Wu

Publications and source records attributed to Ligang Wu.

8 recordsLinked to original sources

PubMed2006

PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits.

Polymorphism in microRNA Target Site (PolymiRTS) database is a collection of naturally occurring DNA variations in putative microRNA target sites. PolymiRTSs may affect gene expression and cause variations in complex phenotypes. The database integrates sequence polymorphism, phenotype and expression microarray data, and characterizes PolymiRTSs as potential candidates responsible for the quantitative trait locus (QTL) effects. It is a resource for studying PolymiRTSs and their implications in phenotypic variations. PolymiRTS database can be accessed at http://compbio.utmem.edu/miRSNP/.

Animals↗

PubMed2006

Distinguishing monosaccharide stereo- and structural isomers with TOF-SIMS and multivariate statistical analysis.

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is utilized to examine the mass spectra and fragmentation patterns of seven isomeric monosaccharides. Multivariate statistical analysis techniques, including principal component analysis (PCA), allow discrimination of the extremely similar mass spectra of stereoisomers. Furthermore, PCA identifies those fragment peaks that vary significantly between spectra. Heavy isotope studies confirm that these peaks are indeed sugar fragments, allow identification of the fragments, and provide clues to the fragmentation pathways. Excellent reproducibility is shown by multiple experiments performed over time and on separate samples. This study demonstrates the combined selectivity and discrimination power of TOF-SIMS and PCA and suggests new applications of the technique including differentiation of subtle chemical changes in biological samples that may provide insights into cellular processes, disease progress, and disease diagnosis.

Mass Spectrometry↗

PubMed2006

Chemical and biological differentiation of three human breast cancer cell types using time-of-flight secondary ion mass spectrometry.

We use time-of-flight secondary ion mass spectrometry (TOF-SIMS) to image and classify individual cells on the basis of their characteristic mass spectra. Using statistical data reduction on the large data sets generated during TOF-SIMS analysis, similar biological materials can be differentiated on the basis of a combination of small changes in protein expression, metabolic activity and cell structure. We apply this powerful technique to image and differentiate three carcinoma-derived human breast cancer cell lines (MCF-7, T47D, and MDA-MB-231). In homogenized cells, we show the ability to differentiate the cell types as well as cellular compartments (cytosol, nuclear, and membrane). These studies illustrate the capacity of TOF-SIMS to characterize individual cells by chemical composition, which could ultimately be applied to detect and identify single aberrant cells within a normal cell population. Ultimately, we anticipate characterizing rare chemical changes that may provide clues to single cell progression within carcinogenic and metastatic pathways.

Amino Acids↗

PubMed2006

MicroRNAs direct rapid deadenylation of mRNA.

MicroRNAs (miRNAs) are ubiquitous regulators of eukaryotic gene expression. In addition to repressing translation, miRNAs can down-regulate the concentration of mRNAs that contain elements to which they are imperfectly complementary. Using miR-125b and let-7 as representative miRNAs, we show that in mammalian cells this reduction in message abundance is a consequence of accelerated deadenylation, which leads to rapid mRNA decay. The ability of miRNAs to expedite poly(A) removal does not result from decreased translation; nor does translational repression by miRNAs require a poly(A) tail, a 3' histone stem-loop being an effective substitute. These findings suggest that miRNAs use two distinct posttranscriptional mechanisms to down-regulate gene expression.

Animals↗

PubMed2006

A modified TMV-based vector facilitates the expression of longer foreign epitopes in tobacco.

Based upon a mutant isolated from tobacco infected with a recombinant tobacco mosaic virus (TMV), a new TMV-based vector was developed in which four to six C-terminal amino acid residues were deleted from the viral coat protein (CP) subunit. The new vector was quite similar to the original TMV-based vector, which all expressed a well characterized epitope peptide F11 (P(142)-A(152)) of VP1 from foot-and-mouth disease virus (FMDV) serotype O in tobacco, in the infectivity, yield of the virus particles and more importantly protective activity of F11 in guinea pigs and swine against the FMDV. Furthermore, the capacity of the length of foreign peptide encoded by this new vector was much improved to successfully express a peptide F25 containing two fused epitopes F14 (R(200)-L(213)) and F11 of FMDV VP1, which was failed using the original vector in tobacco. Although animal assays indicated that such expressed F25 was not as efficient as F11 in the immunity, possibly due to lack of a spacer arm between the two fused epitopes, the new TMV-based vector may meet the requirement of expressing longer foreign peptides for different vaccines and other medicines.

Base Sequence↗

PubMed2005

Micro-RNA regulation of the mammalian lin-28 gene during neuronal differentiation of embryonal carcinoma cells.

Vertebrate genomes each encode hundreds of micro-RNAs (miRNAs), yet for few of these miRNAs is there empirical evidence as to which mRNA(s) they regulate. Here we report the identification of human lin-28 mRNA as a regulatory target of human miR-125b and its homolog miR-125a. Studies of miR-125b function in mouse P19 embryonal carcinoma cells induced to develop into neurons suggest a role for this regulatory miRNA in mammalian neuronal differentiation, since its increased concentration in these cells contributes to lin-28 downregulation. Within the lin-28 3' untranslated region (UTR) are two conserved miRNA responsive elements (miREs) that mediate repression by miR-125b and miR-125a. Simultaneous deletion of both miREs renders the lin-28 3' UTR almost completely insensitive to these miRNAs, indicating that these two miREs are the principal elements in the lin-28 3' UTR that respond to miR-125. At the 3' end of each element is an adenosine residue that makes a significant contribution to function irrespective of its complementarity to the 5'-terminal nucleotide of miR-125. By contrast to most earlier reports of gene repression by other miRNAs that are imperfectly complementary to their targets, lin-28 downregulation by miR-125 involves reductions in both translational efficiency and mRNA abundance. The decrease in the mRNA concentration is achieved by a posttranscriptional mechanism that is independent of the inhibitory effect on translation.

3' Untranslated Regions↗

PubMed2003

Expression of foot-and-mouth disease virus epitopes in tobacco by a tobacco mosaic virus-based vector.

We expressed two immunogenic dominant epitopes of foot-and-mouth disease virus (FMDV) serotype O in tobacco plant using a vector based on a recombinant tobacco mosaic virus (TMV). The recombinant viruses TMVF11 and TMVF14 contained peptides of 11 and 14 amino acid residues, respectively, from FMDV VP 1 fused to the open reading frame of TMV coat protein (CP) gene between amino acid residues 154 and 155. TMVF11 and TMVF14 systemically infected tobacco plant and produced large quantities of stable progeny viral particles assembled with the modified CP subunits. Guinea pigs, mice and swine were used to test the protective effects of the recombinant viruses against FMDV infection. Most guinea pigs were protected against FMDV challenge after parenteral injection with TMVF11, TMVF14, or the mixture TMVF11/TMVF14, but not wtTMV. The TMVF11/TMVF14 mixture protected all animals when challenged with 150 guinea pig 50% infection dosage (GPID(50)) FMDV. Oral administration of the TMVF11/TMVF14 mixture (3mg total) protected 3/8 guinea pigs against the same FMDV challenge. Most of the suckling mice parenterally injected with antiserum from guinea pigs immunized with the TMVF11/TMVF14 mixture, but not with wtTMV, were also protected against FMDV challenge with 10 suckling mouse 50% lethal dosage (SMLD(50)), indicating that antibodies produced in guinea pigs immunized with the TMVF11/TMVF14 mixture specifically neutralized FMDV. Western blot analysis indicated that antiserum from those guinea pigs reacted with the FMDV VP1 protein. The protective effect of TMVF11 was also demonstrated in swine, where preliminary tests showed that nine pigs immunized with TMVF11 in three experiments were protected against FMDV challenge with 20 minimal infecting dose (MID).

Animals↗

PubMed2003

A specific cis-hairpin ribozyme facilitates infection of a TMV-based DNA vector in tobacco protoplasts.

The effect of a specific cis-hairpin ribozyme on TMV-based vectors in the infection of tobacco protoplasts was studied. Vectors contained full-length TMV genome cDNA linked to a T7 promoter or a CaMV 35S promoter at the 5'-end and an NOS gene polyadenylation signal at the 3'-end. The coat protein (CP) gene was replaced with the green fluorescent protein (GFPuv) gene allowing quantification of protoplast infection. In plasmids pTMVGFPRIB (T7-driven) and pSTMVGFPRIB (CaMV 35S-driven), the cDNA fragment of the cis-hairpin ribozyme (designed to specifically cleave the transcripts immediately downstream of the 3'-terminus of TMV RNA) was inserted between the 3'-terminus of TMV genome and NOS sequence. The in vitro transcript TMVGFPRIB was three- to fivefold more infectious than the control TMVGFPNOS. Northern blot analysis indicated that the 3'-terminal non-viral sequence had been cleaved from the in vitro transcripts by the cis-hairpin ribozyme soon after in vitro transcription. pSTMVGFPRIB and pSTMVGFPNOS plasmid DNAs were, as expected, less infectious than their in vitro transcript counterparts. However, pSTMVGFPRIB was somewhat more infectious than pSTMVGFPNOS. Northern blot analysis indicated that pSTMVGFPRIB synthesized more genomic and sub-genomic RNAs in the protoplasts. The significant increase in infectivity and viral RNA synthesis is due to the specific activity of the cis-hairpin ribozyme in vivo. Therefore, the cis-hairpin ribozyme described here may improve TMV-based vectors in the expression of foreign protein in plants.

Base Sequence↗