Biomedical subjects

Hongbin Liu

Publications and source records attributed to Hongbin Liu.

16 recordsLinked to original sources

PubMed2007

Expression of Hand2 is sufficient for neurogenesis and cell type-specific gene expression in the enteric nervous system.

The basic helix-loop-helix DNA binding protein Hand2 is expressed in neural crest-derived precursors of enteric neurons and has been shown to affect both neurogenesis and neurotransmitter specification of noradrenergic sympathetic ganglion neurons. In the current study, our goal was to determine whether Hand2 affects neurogenesis and/or expression of vasoactive intestinal polypeptide and choline acetyltransferase in developing enteric neurons. Gain-of-function of Hand2 in HNK-1(+) immmunoselected precursor cells resulted in increased neurogenesis. The number of neurons expressing vasoactive intestinal polypeptide increased in response to Hand2 overexpression although choline acetyltransferase was not affected. Targeted deletion of Hand2 in neural crest cells resulted in loss of all neurons expressing vasoactive intestinal polypeptide along the length of the gastrointestinal tract, patterning defects in the myenteric plexus of the stomach, and altered number and morphology of neurons expressing TH. Our data demonstrate that expression of Hand2 is sufficient and necessary for neurogenesis and expression of a subset of cell type-specific markers in the developing enteric nervous system.

Animals↗

PubMed2006

Sperm chromatin proteomics identifies evolutionarily conserved fertility factors.

Male infertility is a long-standing enigma of significant medical concern. The integrity of sperm chromatin is a clinical indicator of male fertility and in vitro fertilization potential: chromosome aneuploidy and DNA decondensation or damage are correlated with reproductive failure. Identifying conserved proteins important for sperm chromatin structure and packaging can reveal universal causes of infertility. Here we combine proteomics, cytology and functional analysis in Caenorhabditis elegans to identify spermatogenic chromatin-associated proteins that are important for fertility. Our strategy employed multiple steps: purification of chromatin from comparable meiotic cell types, namely those undergoing spermatogenesis or oogenesis; proteomic analysis by multidimensional protein identification technology (MudPIT) of factors that co-purify with chromatin; prioritization of sperm proteins based on abundance; and subtraction of common proteins to eliminate general chromatin and meiotic factors. Our approach reduced 1,099 proteins co-purified with spermatogenic chromatin, currently the most extensive catalogue, to 132 proteins for functional analysis. Reduction of gene function through RNA interference coupled with protein localization studies revealed conserved spermatogenesis-specific proteins vital for DNA compaction, chromosome segregation, and fertility. Unexpected roles in spermatogenesis were also detected for factors involved in other processes. Our strategy to find fertility factors conserved from C. elegans to mammals achieved its goal: of mouse gene knockouts corresponding to nematode proteins, 37% (7/19) cause male sterility. Our list therefore provides significant opportunity to identify causes of male infertility and targets for male contraceptives.

Animals↗

PubMed2006

The endocrine-disrupting compound, nonylphenol, inhibits neurotrophin-dependent neurite outgrowth.

Endocrine-disrupting compounds (EDCs) may interfere with neuronal development due to high levels of accumulation in biological tissue and potentially aberrant steroid signaling. Treatment of dissociated embryonic Xenopus spinal cord neurons with the EDC, nonylphenol (NP), did not alter cell survival or neurite outgrowth but inhibited neurotrophin-induced neurite outgrowth, effects that were recapitulated by treatment with comparable concentrations of 17 beta-estradiol (E2) and beta-estradiol 6-(O-carboxy-methyl)oxime: BSA (E2-BSA), but not a synthetic androgen. Effects of NP were not inhibited by the nuclear estrogen receptor antagonist, ICI 182,780, but were inhibited by the G protein antagonist, pertussis toxin. Nerve growth factor (NGF)-induced neurite outgrowth in Xenopus neurons was shown to require MAPK signaling. NP did not affect TrkA expression, MAPK signaling, or phosphatidylinositol 3' kinase-Akt-glycogen synthase kinase 3 beta (PI3K-Akt-GSK3 beta) signaling in Xenopus. The ability of NP to inhibit NGF-induced neurite outgrowth without altering survival was recapitulated in the rat pheochromocytoma (PC12) cell line. As with Xenopus neurons, the inhibitory actions of NP in PC12 cells were not antagonized by ICI 182,780 and did not involve alterations in signaling along either the MAPK or PI3K-Akt-GSK3 beta pathways. NP did significantly inhibit the ability of NGF to increase protein kinase A activity in this cell line. These data have important implications with respect to potentially deleterious effects of NP exposure during early neural development and highlight the fact that bioaccumulation of EDCs, such as NP, may elicit very disparate effects along divergent signaling pathways than those that arise from the actions of physiological levels of endogenous estrogens.

Animals↗

PubMed2006

High recovery HPLC separation of lipid rafts for membrane proteome analysis.

Proteomic analysis of complex samples can be facilitated by protein fractionation prior to enzymatic or chemical fragmentation combined with MS-based identification of peptides. Although aqueous soluble protein fractionation by liquid chromatography is relatively straightforward, membrane protein separations have a variety of technical challenges. Reversed-phase high performance liquid chromatography (RP-HPLC) separations of membrane proteins often exhibit poor recovery and bandwidths, and generally require extensive pretreatment to remove lipids and other membrane components. Human brain tissue lipid raft protein preparations have been used as a model system to develop RP-HPLC conditions that are effective for protein fractionation, and are compatible with downstream proteomic analytical workflows. By the use of an appropriate RP column material and operational conditions, human brain membrane raft proteins were successfully resolved by RP-HPLC and some of the protein components, including specific integral membrane proteins, identified by downstream SDS-PAGE combined with in-gel digestion, or in-solution digestion and LC-MS/MS analysis of tryptic fragments. Using the described method, total protein recovery was high, and the repeatability of the separation maintained after repeated injections of membrane raft preparations.

Amino Acid Sequence↗

PubMed2005

BMP4 supports noradrenergic differentiation by a PKA-dependent mechanism.

Differentiation of neural crest-derived noradrenergic neurons depends upon signaling mediated downstream of BMP binding to cognate receptors and involving cAMP. Compiled data from many groups suggest that neurogenesis and cell type-specific noradrenergic marker gene regulation is coordinated through the expression and function of the basic helix-loop-helix DNA binding protein HAND2 and the homeodomain DNA binding protein Phox2a. However, information detailing how BMP-mediated signaling and signaling through cAMP are coordinated has been lacking. We now provide compelling data suggesting that differentiation of noradrenergic sympathetic ganglion neurons depends upon both canonical and non-canonical pathways of BMP-mediated signaling. The non-canonical pathway involves the activation of protein kinase A (PKA) independent of cAMP. This is a novel mechanism in neural crest-derived cells and is necessary to support neurogenesis as well as aspects of DBH promoter regulation involving HAND2 phosphorylation and dimerization. The expression of transcripts encoding HAND2 and Phox2a is regulated via canonical BMP signaling and thus affects both neurogenesis and cell type-specific gene expression. Interestingly, cAMP- and MapK-mediated signaling modulate specific target sites in both the canonical and non-canonical BMP pathways. Activity of MapK is required for HAND2 transcription and thus affects neurogenesis. Signaling affected by cAMP is necessary for the transcription of Phox2a as well as regulation of DBH promoter transactivation by Phox2a and HAND2. We suggest a comprehensive model that shows how BMP- and cAMP-mediated intracellular signaling integrate neurogenesis and cell type-specific noradrenergic marker gene expression and function.

Animals↗

PubMed2004

A model for random sampling and estimation of relative protein abundance in shotgun proteomics.

Proteomic analysis of complex protein mixtures using proteolytic digestion and liquid chromatography in combination with tandem mass spectrometry is a standard approach in biological studies. Data-dependent acquisition is used to automatically acquire tandem mass spectra of peptides eluting into the mass spectrometer. In more complicated mixtures, for example, whole cell lysates, data-dependent acquisition incompletely samples among the peptide ions present rather than acquiring tandem mass spectra for all ions available. We analyzed the sampling process and developed a statistical model to accurately predict the level of sampling expected for mixtures of a specific complexity. The model also predicts how many analyses are required for saturated sampling of a complex protein mixture. For a yeast-soluble cell lysate 10 analyses are required to reach a 95% saturation level on protein identifications based on our model. The statistical model also suggests a relationship between the level of sampling observed for a protein and the relative abundance of the protein in the mixture. We demonstrate a linear dynamic range over 2 orders of magnitude by using the number of spectra (spectral sampling) acquired for each protein.

Data Collection↗

PubMed2004

Dissection of the mammalian midbody proteome reveals conserved cytokinesis mechanisms.

Cytokinesis is the essential process that partitions cellular contents into daughter cells. To identify and characterize cytokinesis proteins rapidly, we used a functional proteomic and comparative genomic strategy. Midbodies were isolated from mammalian cells, proteins were identified by multidimensional protein identification technology (MudPIT), and protein function was assessed in Caenorhabditis elegans. Of 172 homologs disrupted by RNA interference, 58% displayed defects in cleavage furrow formation or completion, or germline cytokinesis. Functional dissection of the midbody demonstrated the importance of lipid rafts and vesicle trafficking pathways in cytokinesis, and the utilization of common membrane cytoskeletal components in diverse morphogenetic events in the cleavage furrow, the germline, and neurons.

Animals↗

PubMed2004

Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases.

The purpose of this work is to develop and verify statistical models for protein identification using peptide identifications derived from the results of tandem mass spectral database searches. Recently we have presented a probabilistic model for peptide identification that uses hypergeometric distribution to approximate fragment ion matches of database peptide sequences to experimental tandem mass spectra. Here we apply statistical models to the database search results to validate protein identifications. For this we formulate the protein identification problem in terms of two independent models, two-hypothesis binomial and multinomial models, which use the hypergeometric probabilities and cross-correlation scores, respectively. Each database search result is assumed to be a probabilistic event. The Bernoulli event has two outcomes: a protein is either identified or not. The probability of identifying a protein at each Bernoulli event is determined from relative length of the protein in the database (the null hypothesis) or the hypergeometric probability scores of the protein's peptides (the alternative hypothesis). We then calculate the binomial probability that the protein will be observed a certain number of times (number of database matches to its peptides) given the size of the data set (number of spectra) and the probability of protein identification at each Bernoulli event. The ratio of the probabilities from these two hypotheses (maximum likelihood ratio) is used as a test statistic to discriminate between true and false identifications. The significance and confidence levels of protein identifications are calculated from the model distributions. The multinomial model combines the database search results and generates an observed frequency distribution of cross-correlation scores (grouped into bins) between experimental spectra and identified amino acid sequences. The frequency distribution is used to generate p-value probabilities of each score bin. The probabilities are then normalized with respect to score bins to generate normalized probabilities of all score bins. A protein identification probability is the multinomial probability of observing the given set of peptide scores. To reduce the effect of random matches, we employ a marginalized multinomial model for small values of cross-correlation scores. We demonstrate that the combination of the two independent methods provides a useful tool for protein identification from results of database search using tandem mass spectra. A receiver operating characteristic curve demonstrates the sensitivity and accuracy level of the approach. The shortcomings of the models are related to the cases when protein assignment is based on unusual peptide fragmentation patterns that dominate over the model encoded in the peptide identification process. We have implemented the approach in a program called PROT_PROBE.

Amino Acid Sequence↗

PubMed2004

Formation and composition of the Bacillus anthracis endospore.

The endospores of Bacillus anthracis are the infectious particles of anthrax. Spores are dormant bacterial morphotypes able to withstand harsh environments for decades, which contributes to their ability to be formulated and dispersed as a biological weapon. We monitored gene expression in B. anthracis during growth and sporulation using full genome DNA microarrays and matched the results against a comprehensive analysis of the mature anthrax spore proteome. A large portion (approximately 36%) of the B. anthracis genome is regulated in a growth phase-dependent manner, and this regulation is marked by five distinct waves of gene expression as cells proceed from exponential growth through sporulation. The identities of more than 750 proteins present in the spore were determined by multidimensional chromatography and tandem mass spectrometry. Comparison of data sets revealed that while the genes responsible for assembly and maturation of the spore are tightly regulated in discrete stages, many of the components ultimately found in the spore are expressed throughout and even before sporulation, suggesting that gene expression during sporulation may be mainly related to the physical construction of the spore, rather than synthesis of eventual spore content. The spore also contains an assortment of specialized, but not obviously related, metabolic and protective proteins. These findings contribute to our understanding of spore formation and function and will be useful in the detection, prevention, and early treatment of anthrax. This study also highlights the complementary nature of genomic and proteomic analyses and the benefits of combining these approaches in a single study.

Bacillus anthracis↗

PubMed2003

A correlation algorithm for the automated quantitative analysis of shotgun proteomics data.

Quantitative shotgun proteomic analyses are facilitated using chemical tags such as ICAT and metabolic labeling strategies with stable isotopes. The rapid high-throughput production of quantitative "shotgun" proteomic data necessitates the development of software to automatically convert mass spectrometry-derived data of peptides into relative protein abundances. We describe a computer program called RelEx, which uses a least-squares regression for the calculation of the peptide ion current ratios from the mass spectrometry-derived ion chromatograms. RelEx is tolerant of poor signal-to-noise data and can automatically discard nonusable chromatograms and outlier ratios. We apply a simple correction for systematic errors that improves the accuracy of the quantitative measurement by 32 +/- 4%. Our automated approach was validated using labeled mixtures composed of known molar ratios and demonstrated in a real sample by measuring the effect of osmotic stress on protein expression in Saccharomyces cerevisiae.

Algorithms↗

PubMed2002

[Effectiveness of post-exposure prophylaxis using live attenuated hepatitis Alpha vaccine (H(2) strain) among schoolchildren].

OBJECTIVE: To observe the efficacy of emergency immunization to abort hepatitis Alpha outbreak using live attenuated hepatitis Alpha vaccine. METHODS: During an outbreak of hepatitis Alpha in a village in Zhengding County, Hebei Province, one dose of live attenuated hepatitis Alpha vaccine (H(2) strain) was administered to 92 schoolchildren of two primary schools in that village on a voluntary basis, and 189 schoolchildren who were not vaccinated were used as controls. Their serum specimens were collected 3 times at different time points (0 and 18 days after the vaccination and 40 days after the appearance of the last hepatitis Alpha case). The total antibody and IgM of hepatitis Alpha were examined by ELISA. Clinical observation was made to discover whether new case appeared. The rates of seroconversion and hepatitis Alpha in susceptibles between vaccinated and unvaccinated groups were compared. RESULTS: The new infection rate of hepatitis Alpha during the 18 days after vaccination was 5.43% in the vaccinated group and 7.43% in the control group (P > 0.05). The prevalence rate was 0 in both groups (P > 0.05). The new infection rate of hepatitis Alpha during the period from the 18th day after vaccination to the 40th day after the appearance of the last case was 2.41% in the vaccinated group and 3.21% in the control group (P > 0.05). CONCLUSION: The live attenuated hepatitis Alpha vaccine can not provide post-exposure protection against infection of hepatitis Alpha virus during the outbreak.

Child↗

PubMed2002

[Immunogenicity and efficacy of two live attenuated hepatitis A vaccines (H(2) strains and LA-1 strains)].

OBJECTIVE: To assess the efficacy and immunogenicity of two live attenuated hepatitis A vaccines. METHODS: Randomized and controlled clinical trials were conducted in Guanxi, Hebei and Shanghai, 457 251 children were enrolled. The efficacy for preventing clinical hepatitis A was calculated by the comparison of incidence rate of disease between vaccine group and control group. Susceptible subjects tested anti-HAV negative before the study were followed up after vaccination for determination of the immunogenicity and vaccine efficacy to prevent subclinical infection. RESULTS: The protective efficacy to prevent clinical infection by both H(2) and LA-1 vaccines were 95%. The peak of seroconversion was observed in 94.9% and 86.0% respectively for the two vaccines. The seroconversion rate decreased to 75% approximately 80% in the third year, but the vaccine protection against clinical hepatitis A has remained unchanged throughout the 3 years. CONCLUSION: Both strains of the live attenuated hepatitis A vaccines have good immunogenicity and high protection against clinical disease, the efficacy to prevent subclinical infection is not significant. The subclinical HAV infection serves as a natural booster for the vaccinees.

Adolescent↗

PubMed2002

[Immediate immunological effect of China-made recombinant hepatitis B vaccine expressed by transgenic Chinese hamster ovary cell line].

OBJECTIVE: To understand the protective efficacy of China-made recombinant hepatitis B vaccine expressed by transgenic Chinese hamster ovary cell line among newborns. METHODS: 2 969 newborns in seven townships in Zhengding County, Hebei Province, were vaccinated with 10 microgram x 3 doses of China-made recombinant hepatitis B vaccine expressed by transgenic Chinese hamster ovary cell line according to the 0 - 1 - 6 month schedule from 1 January 1997 to 31 August 1999. The newborns were to be vaccinated with the first dose within 24 hours after they were born. 1906 serum samples were selected in April 2000 to detect the hepatitis B infection markers, including HBsAg, HBsAb and HbcAb by RIA kits. RESULTS: 2 783 of the 2 969 newborns (93.74%) were vaccinated with three doses, 2 833 of them (95.42%) were vaccinated with the first dose within 24 hours after they were born. The anti-HBs positive rate was 98.25% (S/N >/= 2.1) or 94.26% (S/N >/= 10.0), and the geometric mean titer (GMT) value of antibody was 77.64 within the first year after the whole course vaccination. Then the antibody level decreased gradually with the lapse of time. The HBsAb positive rate was 92.31% (S/N >/= 2.1) or 68.96% (S/N >/= 10.0), and GMT value was 22.86 within the third year after vaccination. The HBsAg positive rates remained less than 1%, the HBcAb positive rates and HBV infection rates remained 1% approximately 3% within 3 years after vaccination. CONCLUSION: The protective efficacy of China-made recombinant hepatitis B vaccine is satisfactory.

Animals↗

PubMed2002

Multidimensional separations for protein/peptide analysis in the post-genomic era.

Proteomics is the study of all or part of the protein complement of genes in an organism, often involving the analysis of complex protein/peptide samples. Such complex samples are beyond the separation capacity of 1-D separation techniques. This review describes several multidimensional separations for proteins and peptides. First, several variants of 2-D liquid chromatography (2DLC) are reviewed, including coupled size exclusion-reversed phase, ion exchange-reversed phase, and reversed phase-reversed phase chromatography. Second, we describe coupled liquid chromatography and capillary electrophoresis methods. Finally, a multidimensional protein identification technique (MudPIT) is explained in detail. Each of the described techniques has a much higher separation capacity than 1-D methods and can potentially be automated for high-throughput experiments. In particular, MudPIT takes advantage of both the high separation capacity of 2DLC and the powerful peptide characterization ability of tandem mass spectrometry to analyze complex protein samples. Additional applications and developments of multidimensional liquid separations for proteomics are expected in the future.

Chromatography, Affinity↗

PubMed2002

[Long-term efficacy and persistence of Chinese infants after receiving only active plasma-derived hepatitis B vaccine].

BACKGROUND: To determine the long-term efficacy and persistence of Chinese infants after receiving only active plasma-derived hepatitis B vaccine, and to evaluate if providing booster vaccination after basic hepatitis B immunization is necessary. METHODS: Infants who were born in 1986-1988 in four demonstrative hepatitis B immunization trial areas of Hunan, Guangxi, Hebei and Shanghai after receiving only active plasma-derived hepatitis B vaccination, had been randomly followed up for 15 years. HBsAg,anti-HBs and anti-HBc in 21 680 person-times were tested using commercial SPRIA kits. RESULTS: Prevalence of HBV carriers was less than 1.66% among all children vaccinated with only active plasma-derived hepatitis B vaccine in 4 clinical trial areas. Prevalence of HBsAg did not increase with years after vaccination,90%(95% Cl:83.1%-97.2%) effectiveness of hepatitis B vaccine persisted for 15 years in preventing chronic HBV infection. Carriage, HBV infection and efficacy were not different among all age groups (P>0.05). Seroprotection rate (anti-HBs?10 mIU/ml) and quantity of anti-HBs were significantly decreased with years after vaccination. Seroprotection rates of anti-HBs were 40%-50% and 30%-42% during the 9th-10th year and the 13th-14th ear of vaccination, respectively. Titer of anti-HBs declined?by 90% after 14 years. CONCLUSIONS: These results showed that long-term efficacy of only active plasma-derived hepatitis B vaccination, which was not affected by decline in seroprotection rate and titer of anti-HBs. For children and adults whose immune status is normal, booster doses of vaccine are not recommended.

Adolescent↗

PubMedDate not supplied

Reversed-phase high-performance liquid chromatographic prefractionation of immunodepleted human serum proteins to enhance mass spectrometry identification of lower-abundant proteins.

Serum analysis represents an extreme challenge due to the dynamic range of the proteins of interest, and the high structural complexity of the constituent proteins. In serum, the quantities of proteins and peptides of interest range from those considered "high abundance", present at 2-70% by mass of total protein, to those considered "low abundance", present at 10(-12) M or less. This range of analytical target molecules is outside the realm of available technologies for proteomic analysis. Therefore, in this study, we have developed a workflow toward addressing the complexity of these samples through the application of multidimensional separation techniques. The use of reversed-phase methods for the separation and fractionation of protein samples has been investigated, with the goal of developing an optimized serum separation for application to proteomic analysis. Samples of human serum were depleted of the six most abundant proteins, using an immunoaffinity LC method, then were separated under a variety of reversed-phase (RP) conditions using a macroporous silica C18 surface modified column material. To compare the qualities of the RP separations of this complex protein sample, absorbance chromatograms were compared, and fractions were collected for off-line SDS-PAGE and 2D-LC-MS/MS analysis. The column fractions were further investigated by determination of protein identities using either whole selected fractions, or gel bands excised from SDS-PAGE gels of the fractions. In either case samples underwent tryptic fragmentation and peptide analysis using MALDI-MS or LC-MS/MS. The preferred conditions for RP protein separation exhibited reproducibly high resolution and high protein recoveries (>98%, as determined by protein assay). Using the preferred conditions also permitted high column mass load, with up to 500 microg of protein well tolerated using a 4.6 mm ID x 50 mm column, or up to 1.5 mg on a 9.4 mm ID x 50 mm column. Elevated column temperature (80 degrees C) was observed to be a critical operational parameter, with poorer results observed at lower temperatures. The combination of sample simplification by immunoaffinity depletion combined with a robust and high recovery RP-HPLC fractionation yields samples permitting higher quality protein identifications by coupled LC-MS methods.

Amino Acid Sequence↗