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Xin Liu

Publications and source records attributed to Xin Liu.

At least 37 records · Page 2Linked to original sources
PubMed2006

Mass spectrometry-based glycomics strategy for exploring N-linked glycosylation in eukaryotes and bacteria.

N-Glycosylation of proteins is recognized as one of the most common posttranslational modifications in eukaryotes. To date, most glycomics techniques are limited to examining eukaryotic pathways. Technologies capable of characterizing newly described N-linked glycosylation systems in bacteria from biologically relevant samples in an accurate, rapid, and cost-effective manner are needed. In this paper, a new glycomics strategy, based on the combination of nonspecific proteolytic digestion and permethylation, was devised that can be used for both eukaryotic and bacterial glycoproteins. Eukaryotic glycoproteins were digested with Pronase E with a higher ratio (enzyme/protein, 2:1-3:1) and a longer reaction time (48-72 h). The Asn-glycans were then purified using porous graphitic carbon cartridges followed by permethylation. The mass spectrometric data indicated that hydroxyl groups were methylated, while the amino group in asparagine underwent beta-elimination. Both modifications were evident from an increase of 111 Da in the molecular masses of permethylated Asn-glycans compared to the corresponding free oligosaccharides. NMR spectroscopy corroborated these results by showing that the mass difference resulted from beta-elimination of the free amino group in the asparagine residue. The method was validated with the characterization of the N-linked glycoproteins in total protein extracts from the bacterium Campylobacter jejuni 11168H. In addition to detecting the Asn-linked bacterial heptasaccharide, we also observed an unexpected free heptasaccharide intermediate that required a functional glycosylation pathway. These results demonstrate the usefulness of this method for screening N-linked glycans expressed by eukaryotes and bacteria and for detecting novel intermediates of N-linked glycosylation pathways.

Animals↗
PubMed2006

Nonsteroidal antiinflammatory drugs and decreased risk of advanced prostate cancer: modification by lymphotoxin alpha.

The potentially protective effect of nonsteroidal antiinflammatory drugs (NSAIDs) on prostate cancer may only exist among certain subgroups of men, such as those with particular variants in inflammatory response genes. To investigate this, the authors undertook a case-control study (n = 1,012) of the association between NSAIDs and more advanced prostate cancer in Ohio men recruited between 2001 and 2004 and evaluated whether this association was modified by a functional polymorphism in the lymphotoxin alpha (LTA) gene (LTA C+80A, where the CC genotype results in higher LTA production). The authors observed an inverse association between aspirin or ibuprofen use and disease (odds ratio = 0.67, 95% confidence interval: 0.52, 0.87). This was modified by the LTA C+80A variant (p for interaction = 0.03): Among men with the CC genotype, the inverse association between NSAIDs and prostate cancer was substantially stronger (odds ratio = 0.43, 95% confidence interval: 0.28, 0.67). For men without the CC genotype, NSAID use was not associated with disease (p = 0.30). The authors observed similar associations when examining dose/duration of NSAID use. This suggests that any potential chemoprevention of prostate cancer by NSAIDs may be most appropriate for men with the LTA +80CC genotype.

Adult↗
PubMed2006

Determination of ergosterol in ganoderma spore lipid from the germinating spores of Ganoderma lucidum by high-performance liquid chromatography.

A gradient reversed-phase high-performance liquid chromatography (HPLC) method was developed for the separation and determination of free ergosterol in ganoderma spore lipid (GSL) extracted from the sporoderm-broken germinating spores of Ganoderma lucidum. Sodium hydroxide in methanol was added for the hydrolysis of ergosteryl esters to determine the total content of ergosterol in GSL by HPLC. A 0.04 M concentration of sodium hydroxide in reaction mixtures was appropriate for the complete hydrolysis of ergosteryl esters without a significant loss of ergosterol during saponification. In addition, the ergosterol content in four commercial GSL softgel supplements from four different firms was determined. The results showed that the ergosterol content in these samples had significant differences. Ergosterol content may be a suitable marker for evaluating the quality of GSL products.

Chromatography, High Pressure Liquid↗
PubMed2006

The genomic termini of wild-type and vaccine strains of measles virus.

The genomic termini from 18 strains of measles virus (MV) including wild-type MVs from the pre-vaccine period, recent wild-type isolates and various vaccine strains were sequenced. The first 25 nucleotides of the 3' terminus and last 52 nucleotides of the 5' terminus were conserved in all of the viruses examined. Nucleotides 26 and 42 of the 3' leader were A and G, respectively, in all genotype A viruses except Edmonston wild-type (Ed-WT). All non-genotype A viruses and Ed-WT had U in both positions. No consistent substitution pattern was found in the 5' trailer region of the genome. The nucleotide substitutions at positions 26 and 42 in the 3' leader region were introduced into a MV-CAT mini-genome to test for their effect on the production of reporter protein in both a vaccinia T7-driven, plasmid-based replication assay as well as in a helper virus system. Regardless of the source of the polymerase proteins or the natural leader sequence of the helper viruses, the mini-genome 26A42G produced more CAT protein than 26U42U. The nucleotide substitution at 26 had the greatest effect on CAT production. These results indicated that naturally occurring nucleotide variations in the 3' leader region can affect the levels of reporter protein synthesis, and presumably affected the level of replication of the virus.

3' Untranslated Regions↗
PubMed2006

Identification of amino acid residues involved in the interaction between measles virus Haemagglutin (MVH) and its human cell receptor (signaling lymphocyte activation molecule, SLAM).

Signaling lymphocyte activation molecule (SLAM; also known as CD150) is a newly identified cellular receptor for measles virus (MV). The interaction between MV Haemagglutin (MVH) and SLAM is an initial step for MV entry. We have identified several novel SLAM binding sites at residues S429, T436 and H437 of MVH protein and MVH mutants in these residues dramatically decrease the ability to interaction with the cell surface SLAM and fail to coprecipitation with SLAM in vivo as well as malfunction in syncytium formation. At the same time, K58, S59 and H61 of SLAM was also identified to be critical for MVH and SLAM binding. Further, these residues may be useful targets for the development of measles therapy.

Animals↗
PubMed2006

Extremely low penetrance of deafness associated with the mitochondrial 12S rRNA T1095C mutation in three Chinese families.

Mutations in mitochondrial DNA (mtDNA) have been found to be associated with sensorineural hearing loss. We report here the clinical, genetic, and molecular characterization of three Chinese pedigrees (a total of 43 matrilineal relatives) with aminoglycoside-induced impairment. Clinical evaluation revealed the variable phenotype of hearing impairment including audiometric configuration in these subjects, although these subjects shared some common features: being bilateral and sensorineural hearing impairment. Strikingly, only probands of these Chinese pedigrees exhibited severe to profound hearing loss. Mutational analysis of the mtDNA in these pedigrees showed the presence of homoplasmic 12S rRNA T1095C mutation, which has been associated with hearing impairment in several families. Sequence analysis of the complete mitochondrial genomes in these pedigrees showed the identical homoplasmic T1095C mutation and distinct sets of mitochondrial DNA (mtDNA) variants belonging to haplogroups M11C. Despite the presence of several highly evolutionarily conservative variants in protein-encoding genes and 16S rRNA gene, the extremely low penetrance of hearing loss with the T1095C mutation implies that the mitochondrial variants may not play an important role in the phenotypic expression of the T1095C mutation in these Chinese families. However, the history of exposure to aminoglycosides in these three hearing-impaired subjects suggested that the aminoglycosides very likely are the cause of hearing loss.

China↗
PubMed2006

Characterization of the HMW glutenin subunits from Aegilops searsii and identification of a novel variant HMW glutenin subunit.

High molecular weight (HMW) glutenin subunits are conserved seed storage proteins in wheat and related species. Here we describe a more detailed characterization of the HMW glutenin subunits from Aegilops searsii, which is diploid and contains the S(s) genome related to the S genome of Aegilops speltoides and the A, B and D genomes of hexaploid wheat. SDS-PAGE experiments revealed two subunits (one x and one y) for each of the nine Ae. searsii accessions analyzed, indicating that the HMW glutenin subunit gene locus of Ae. searsii is similar to the Glu-1 locus found in wheat in containing both x and y genes. The primary structure of the four molecularly cloned subunits (from two Ae. searsii accessions) was highly similar to that of the previously reported x and y subunits. However, in one accession (IG49077), the last 159 residues of the x subunit (1S(s)x49077), which contained the sequence element GHCPTSPQQ, were identical to those of the y subunit (1S(s)y49077) from the same accession. Consequently, 1S(s)x49077 contains an extra cysteine residue located at the C-terminal part of its repetitive domain, which is novel compared to the x-type subunits reported so far. Based on this and previous studies, the structure and expression of the Glu-1 locus in Ae. searsii is discussed. A hypothesis on the genetic mechanism generating the coding sequence for the novel 1S(s)x49077 subunit is presented.

Amino Acid Sequence↗
PubMed2006

Genetic background controls tumor development in PTEN-deficient mice.

PTEN is one of the most frequently mutated tumor suppressor genes in human cancers. Germ line mutations of PTEN have been detected in three rare autosomal-dominant disorders. However, identical mutations in the PTEN gene may lead to different symptoms that have traditionally been described as different disorders, such as Cowden disease, Lhermitte-Duclos disease, and Bannayan-Zonana syndromes. This lack of genotype-phenotype correlation prompted us to directly test the possible effects of genetic background or modifier genes on PTEN-controlled tumorigenesis using genetically engineered mouse models. In this study, we generated two animal models in which either exon 5 (Pten(Delta5)) or promoter to exon 3 (Pten(-)) of the murine Pten gene were deleted and compared phenotypes associated with individual mutations on two genetic backgrounds. We found that the onset and spectrum of tumor formation depend significantly on the genetic background but less on the type of mutation generated. Our results suggest that PTEN plays a critical role in cancer development, and genetic background may influence the onset, the spectrum, and the progression of tumorigenesis caused by Pten mutation.

Alleles↗
PubMed2006

Structural features in carrageenan that interact with a heparin-binding hematopoietic growth factor and modulate its biological activity.

The effects of carrageenans' structural features on its interaction with granulocyte colony-stimulating factor (G-CSF) and on the growth and differentiation of a G-CSF dependent leukemia cell line (NFS-60) were studied. lambda, iota, and kappa carrageenans, with decreasing contents of sulfation, bound to G-CSF with binding constants of (6.2+/-0.6) x 10(5)M(-1), (7.4+/-0.5) x 10(5)M(-1) and (6.0+/-0.4) x 10(5)M(-1), and with 27.7+/-0.2, 17.4+/-0.1 and 8.4+/-0.1 binding sites, respectively. However, kappa carrageenan oligosaccharide had no affinity for G-CSF. The three carrageenans significantly inhibited G-CSF-induced growth of NFS-60 cells. The high sulfate content lambda carrageenan could also induce the maturation of the cells, but relatively low sulfate content iota and kappa carrageenans could not. The results suggested that G-CSF-carrageenan bindings were dependent on carrageenans' sulfate contents and chain lengths, which could also affect the growth and differentiation of NFS-60 cells.

Carbohydrate Conformation↗
PubMed2006

Hsc70 contacts helix III of the J domain from polyomavirus T antigens: addressing a dilemma in the chaperone hypothesis of how they release E2F from pRb.

Hsc70's expected binding site on helix II of the J domain of T antigens appears to be blocked in its structure bound to tumor suppressor pRb. We used NMR to map where mammalian Hsc70 binds the J domain of murine polyomavirus T antigens (PyJ). The ATPase domain of Hsc70 unexpectedly has its biggest effects on the NMR peak positions of the C-terminal end of helix III of PyJ. The Hsc70 ATPase domain protects the C-terminal end of helix III of PyJ from an uncharged paramagnetic probe of chelated Gd(III), clearly suggesting the interface. Effects on the conserved HPD loop and helix II of PyJ are smaller. The NMR results are supported by a novel assay of Hsc70's ATP hydrolysis showing that mutations of surface residues in PyJ helix III impair PyJ-dependent stimulation of Hsc70 activity. Evolutionary trace analysis of J domains suggests that helix III usually may join helix II in contributing specificities for cognate hsp70s. Our novel evidence implicating helix III differs from evidence that Escherichia coli DnaK primarily affects helix II and the HPD loop of DnaJ. We find the pRb-binding fragment of E2F1 to be intrinsically unfolded and a good substrate for Hsc70 in vitro. This suggests that E2F1 could be a substrate for Hsc70 recruited by T antigen to an Rb family member. Importantly, our results strengthen the chaperone hypothesis for E2F release from an Rb family member by Hsc70 recruited by large T antigen. That is, it now appears that Hsc70 can freely access helix III and the HPD motif of large T antigen bound to an Rb family member.

Adenosine Triphosphatases↗
PubMed2006

[Large-scale screening of mtDNA A1555G mutation in China and its significance in prevention of aminoglycoside antibiotic induced deafness].

OBJECTIVE: To explore the necessity of large-scale screening of mtDNA A1555G mutation in prevention of aminoglycoside antibiotic induced deafness (AAID) and to develop a feasible method to prevent AAID. METHODS: A total of 1836 patients with non-syndromic hearing impairment (NSHI), 1352 students of schools for deaf-mutes in 11 provinces and municipality in China, 413 out-patients, and 71 persons from the families with maternal relatives suffering from AAID, underwent questionnaire survey and/or PCR for A-to-G mutation at nucleotide 1555 of the mitochondrial genome. RESULTS: Sixty three patients with mtDNA A1555G mutation were found among the 1836 NSHI patients. Fifty-two maternal pedigrees were identified. 536 cases with normal hearing from these pedigrees were informed to avoid using aminoglycoside antibiotics (AmAn). CONCLUSION: Large-scale screening of mtDNA A1555G mutation and relevant health education to avoid use of AmAn are effective to prevent ototoxicity in the A1555G carriers and their maternal relatives.

Adolescent↗
PubMed2006

Identification of two phosphatidylinositol/phosphatidylcholine transfer protein genes that are predominately transcribed in the flowers of Arabidopsis thaliana.

The Sec14 protein (Sec14p) and its homologs are involved in the transfer of phosphatidylinositol/phosphatidylcholine phospholipids in eukaryotic cells. In the completely sequenced genome of Arabidopsis thaliana, multiple genes encoding putative Sec14p homologs have been predicted based on bioinformatic analysis. Here we report the identification of two yeast Sec14-like genes (designated as AtSFH3 and AtSFH12, respectively) that are predominately transcribed in Arabidopsis flowers. The deduced amino acid sequences of AtSfh3p and AtSfh12p exhibited high similarity to that of Sec14p. Ectopic expression of AtSfh3p or AtSfh12p corrected the high temperature sensitive phenotype caused by Sec14p functional deficiency in Saccharomyces cerevisiae, indicating that the two plant homologs are functional in the intracellular environment. AtSFH3 transcripts were detected in flowers, stems and immature siliques but not roots and leaves, with a relatively higher transcript level in the flowers. In contrast, AtSFH12 transcripts were only detectable in the flowers. Based on histochemical staining of beta-glucuronidase (GUS) activities in the transgenic Arabidopsis plants harboring promoter::GUS constructs, AtSFH3 transcription was first detected in the stigma papillae of the flowers at stage 11, and then in the pollen grains before and after fertilization. On the other hand, AtSFH12 transcription was only found in the mature and germinating pollen grains. The information from this study may provide useful clue for further analysis of the function of plant Sec14p homologs in the development of the male gametic cells and/or the fertilization process in higher plants.

Arabidopsis↗
PubMed2006

Opioid receptor binding and antinociceptive activity of the analogues of endomorphin-2 and morphiceptin with phenylalanine mimics in the position 3 or 4.

Endomorphin-2 (EM-2) and morphiceptin are the same class of putative mu-opioid receptor ligands. To investigate the effectiveness of phenylglycine (Phg, L or D) and homophenylalanine (Hfe) as the surrogates of phenylalanine in the position 3 and/or 4 of them, a series of their analogues were synthesized. Opioid receptor binding affinities were determined. Two analogues, [Hfe3]EM-2 and [Phg4] (EM-2/morphiceptin), showed different but potent antinociceptive activity in mouse hot-plate test, the results combined with their half-lives of degradation by mouse brain homogenate could also present some evidence to the in vivo degradative mechanism of EM-2.

Analgesics↗
PubMed2006

A mechanism-based inactivator for histone demethylase LSD1.

Histone demethylase LSD1 is a flavin-dependent amine oxidase that catalyzes the oxidative removal of one or two methyl groups from the methyl-lysine-4 side chain of histone H3. We have designed and synthesized two peptide-based inhibitor analogues that block LSD1. One of these inhibitors, compound 1, contains a propargylamine functionality and shows time-dependent inactivation of LSD1. Peptide substrate, diMeK4H3-21, protected LSD1 against inactivation by 1 in a concentration-dependent fashion. Mass spectrometric analysis showed that 1 forms a covalent interaction with FAD. Compound 1 did not detectably inhibit monoamine oxidase B in the concentration range studied. Compound 1 is thus a selective, mechanism-based inactivator of LSD1 and is likely to serve as a useful tool in the study of histone modifications and chromatin remodeling.

Amino Acid Sequence↗
PubMed2006

Spectroscopic studies of the interaction between hypocrellin B and human serum albumin.

Previous work has proved that hypocrellin B (HB) binds to human serum albumin (HSA) at a specific site instead of distributed randomly on the surface of a protein. In the current work, further investigation by using bilirubin as a site I marker indicates that HB can compete for the same site with bilirubin, suggesting that the HB binding site is located at sub-domain IIA (site I) of HSA. Moreover, bound to HSA, the HB fluorescence was found to be pH sensitive in physiological range (pH 6.0-8.0). The increasing of binding constant of HB to HSA in the pH range 6-8 also indicates that the N<-->B transition modulates the microenvironment changes of the binding site and influences considerably the binding between HB and HSA. Furthermore, picosecond time-resolved fluorescence spectra of HB-HSA complex in PBS indicate an additional short-lived component compared to that for HB in benzene, which may be assigned to the process of electron transfer from Trp-214 to HB.

Bilirubin↗
PubMed2006

Polymorphisms in estrogen bioactivation, detoxification and oxidative DNA base excision repair genes and prostate cancer risk.

To date, the potential impact of hormones on prostate cancer has predominantly focused on receptor-mediated events. However, catechol estrogens, if not inactivated by catechol-O-methyltransferase (COMT), can generate large quantities of reactive oxygen species (ROS). ROS may cause a spectrum of damage including oxidative DNA base lesions, which can lead to irreversible mutation(s) if they are not repaired by base excision repair (BER) systems. hOGG1 is a key enzyme in short patch BER because it recognizes and performs initial excision of the most common form of oxidative DNA base damage, 8-hydroxyguanine (8-oxo-dG). To investigate potential non-receptor-mediated estrogen effects, we evaluated the association between COMT Val158Met and hOGG1 Ser326Cys polymorphisms and prostate cancer in a family-based case-control study (439 prostate cancer cases, 479 brother controls). We observed no noteworthy associations between these polymorphisms and prostate cancer risk in the total study population. However, among men with more aggressive prostate cancer, the hOGG1 326 Cys/Cys genotype was inversely associated with disease (OR=0.30; 95% CI=0.09-0.98). Combining the lower activity CYP1B1 432 Leu/Leu or Leu/Val genotypes (which may decrease the level of catechol estrogens and ROS generated) with the hOGG1 326 Cys/Cys genotype and the XRCC1 399 Arg/Arg or Arg/Gln genotypes (which may enhance BER) resulted in an even further reduced risk in Caucasians with more aggressive disease (OR=0.09; 95% CI=0.01-0.56). Including the high-activity COMT 158Val allele to this combination also lowered aggressive prostate cancer risk but the effect was not as strong (OR=0.20; 95% CI=0.05-0.88). The decreased risk we observed with the hOGG1 326 Cys/Cys genotype confirms an earlier report and the further reduced risk found with the CYP1B1 (432 Leu/Leu or Leu/Val)-hOGG1 (326 Cys/Cys)-XRCC1 (Arg/Arg or Arg/Gln) genotype combination may lend new insights to the importance of ROS generated from non-receptor-mediated estrogenic mechanisms in more aggressive prostate cancer.

Aged↗