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Hui Ge

Publications and source records attributed to Hui Ge.

16 recordsLinked to original sources
PubMed2007

Association of MTHFR C677T and SHMT(1) C1420T with susceptibility to ESCC and GCA in a high incident region of Northern China.

OBJECTIVE: To assess the association between the C to T transition in the methylenetetrahydro folate reductase gene (MTHFR C677T) and the C to T transition in the serine hydroxymethyltransferase ( 1 )gene (SHMT ( 1 ) C1420T) and the increased risk of carcinogenesis of esophageal squamous cell carcinoma (ESCC) and gastric cardia adenocarcinoma (GCA) in a population of high incident region of Northern China. METHODS: The polymorphisms were genotyped by polymerase chain reaction-restriction fragment length polymorphism and PCR-confronting two-pair primers analysis respectively among 1051 cancer patients (584 ESCC and 467 GCA) and 540 healthy controls. RESULTS: The MTHFR 677T/T genotype significantly increased susceptibility to both ESCC and GCA compared with the C/C genotype, the adjusted OR was 2.13 (95% CI = 1.50-3.02) and 1.28 (95% CI = 1.07-1.53, respectively. For the SHMT ( 1 ) C1420T polymorphism, the C/C genotype was significantly associated with the increased risk of ESCC and GCA, compared with the C/T genotype (the adjusted OR = 1.43 and 1.35, 95% CI = 1.02-2.00 and 1.11-1.63, respectively). The interactive influence of the MTHFR and SHMT ( 1 ) polymorphisms in the risk of ESCC and GCA was also observed. CONCLUSION: The association between the MTHFR C677T and SHMT ( 1 ) C1420T polymorphisms and the risk of ESCC and GCA was demonstrated.

Adenocarcinoma↗
PubMed2006

Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans.

We sequenced approximately 400,000 small RNAs from Caenorhabditis elegans. Another 18 microRNA (miRNA) genes were identified, thereby extending to 112 our tally of confidently identified miRNA genes in C. elegans. Also observed were thousands of endogenous siRNAs generated by RNA-directed RNA polymerases acting preferentially on transcripts associated with spermatogenesis and transposons. In addition, a third class of nematode small RNAs, called 21U-RNAs, was discovered. 21U-RNAs are precisely 21 nucleotides long, begin with a uridine 5'-monophosphate but are diverse in their remaining 20 nucleotides, and appear modified at their 3'-terminal ribose. 21U-RNAs originate from more than 5700 genomic loci dispersed in two broad regions of chromosome IV-primarily between protein-coding genes or within their introns. These loci share a large upstream motif that enables accurate prediction of additional 21U-RNAs. The motif is conserved in other nematodes, presumably because of its importance for producing these diverse, autonomously expressed, small RNAs (dasRNAs).

Animals↗
PubMed2006

Temperature-controlled release of diols from N-isopropylacrylamide-co-acrylamidophenylboronic acid microgels.

N-Isopropylacrylamide-co-acrylamidophenylboronic acid (NIPAM-co-PBA) microgels were prepared by free radical polymerization in water. The release of glucose and Alizarin Red S (ARS) from the microgels as a function of temperature has been investigated by using laser light scattering (LLS) and ultrasensitive differential scanning calorimetry (US-DSC). Such microgels can bind glucose and ARS via boronic acids at a lower temperature. As the temperature increases, the microgels shrink, and the diols are released. The release could be controlled by temperature. The effect of the structure of the microgels on the release is also discussed.

Acrylamides↗
PubMed2006

Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo.

MOTIVATION: Gene expression profiling is a powerful approach to identify genes that may be involved in a specific biological process on a global scale. For example, gene expression profiling of mutant animals that lack or contain an excess of certain cell types is a common way to identify genes that are important for the development and maintenance of given cell types. However, it is difficult for traditional computational methods, including unsupervised and supervised learning methods, to detect relevant genes from a large collection of expression profiles with high sensitivity and specificity. Unsupervised methods group similar gene expressions together while ignoring important prior biological knowledge. Supervised methods utilize training data from prior biological knowledge to classify gene expression. However, for many biological problems, little prior knowledge is available, which limits the prediction performance of most supervised methods. RESULTS: We present a Bayesian semi-supervised learning method, called BGEN, that improves upon supervised and unsupervised methods by both capturing relevant expression profiles and using prior biological knowledge from literature and experimental validation. Unlike currently available semi-supervised learning methods, this new method trains a kernel classifier based on labeled and unlabeled gene expression examples. The semi-supervised trained classifier can then be used to efficiently classify the remaining genes in the dataset. Moreover, we model the confidence of microarray probes and probabilistically combine multiple probe predictions into gene predictions. We apply BGEN to identify genes involved in the development of a specific cell lineage in the C. elegans embryo, and to further identify the tissues in which these genes are enriched. Compared to K-means clustering and SVM classification, BGEN achieves higher sensitivity and specificity. We confirm certain predictions by biological experiments. AVAILABILITY: The results are available at http://www.csail.mit.edu/~alanqi/projects/BGEN.html.

Algorithms↗
PubMed2006

Toward a global picture of development: lessons from genome-scale analysis in Caenorhabditis elegans embryonic development.

Development is the result of complex events, including cascades of transcriptional programs and numerous molecular interactions. Traditionally, research focus has been given to the characterization of individual mutants, regulators, or interactions. With the availability of complete genome sequences and high-throughput (HT) experimental techniques, probing development on a system level has become feasible. Pioneering work initiated in invertebrate model systems such as Caenorhabditis elegans has provided first drafts of catalogs of essential components, transcriptional regulatory diagrams and molecular interaction networks underlying developmental processes. Integrating these drafts approximates a system-level picture of development and provides local models for protein/gene functions. Here we summarize the progress toward elucidating developmental processes on a system level, including the applications of genomic technologies and computational analyses. We discuss C. elegans embryonic development in case studies to illustrate how various HT approaches can be integrated and how biological insights can be gained from these approaches.

Animals↗
PubMed2006

[Correlations between serine hydroxymethyltransferase1 C1420T polymorphisms and susceptibilities to esophageal squamous cell carcinoma and gastric cardiac adenocarcinoma].

BACKGROUND & OBJECTIVE: Serine hydroxymethyltransferase (SHMT), a key enzyme in the folate metabolism, affects gene methylation and DNA synthesis through providing one-carbon units for purine, thymidylate, and methionine. It is closely related to the development and progression of tumors. This study was to investigate the correlations between SHMT1 C1420T single nucleotide polymorphisms (SNP) and susceptibilities to esophageal squamous cell carcinoma (ESCC) and gastric cardiac adenocarcinoma (GCA). METHODS: SHMT1 C1420T SNP was genotyped by polymerase chain reaction-confronting two-pair primers (PCR-CTPP) analysis in 584 ESCC patients, 467 GCA patients, and 540 healthy controls. The correlations between SHMT1 C1420T SNP polymorphisms and susceptibilities to ESCC and GCA were analyzed with Logistic regression model. RESULTS: Family history of upper gastrointestinal cancer (UGIC) significantly enhanced the risk of developing ESCC and GCA [the age, gender, smoking status, and family history of UGIC adjusted odds ratio (OR)=2.89, 95% confident interval (CI)=2.23-3.73; OR =1.68, 95% CI=1.28-2.23]. The frequency of 1420C/T genotype was significantly lower in ESCC and GCA patients than in healthy controls (12.0% vs. 16.5%, P<0.05; 10.9% vs. 16.5%, P<0.01). Compared with C/C genotype, C/T genotype significantly reduced susceptibilities to ESCC and GCA, with adjusted OR of 0.70 (95% CI=0.50-0.98) for ESCC and 0.55 (95% CI=0.38-0.81) for GCA. Stratification analysis showed that C/T genotype significantly reduced susceptibilities to ESCC and GCA among non-smokers, with adjusted OR of 0.54 (95% CI=0.33-0.90) for ESCC and 0.56 (95% CI=0.33-0.95) for GCA. In addition, C/T genotype significantly reduced susceptibility to GCA among individuals with or without UGIC history, with adjusted OR of 0.46 (95%CI=0.24-0.90) and 0.62 (95% CI=0.38-0.99) respectively, and reduced susceptibility to ESCC only among individuals with UGIC history, with adjusted OR of 0.51 (95% CI=0.29-0.89). CONCLUSION: SHMT1 1420C/T genotype could significantly reduce susceptibilities to ESCC and GCA among individuals from high risk areas in Hebei Province of China.

Adenocarcinoma↗
PubMed2006

[Study on the quality of death-case-reporting-system in county and above levels' medical institutions in 2004].

OBJECTIVE: To study the quality of reporting network system on death cases among county and above levels' medical institutions. METHODS: Data on variables related to county reporting rate, unit reporting rate, timeliness of reporting, eligibility rate of reporting, auditing rate, timeliness of auditing, eligibility rate of auditing, percentage of reporting deaths of medical institutes to deaths among total population, percentage of reporting deaths of county and above levels' medical institutes to deaths among estimated deaths at these institutes were collected and distribution of common coding errors was applied to the assessment of reporting deaths. RESULTS: The total reporting rates were: 82.58% at the county level, 42.79% at the units with auditing rate as 96.96%. The eligibility rate of reporting was 69.10% with eligibility rate of auditing as 73.58%. The percentage of reporting deaths from medical institutes to deaths among total population was 8.91%, and the percentage of reporting deaths of county and above levels' medical institutes to deaths among estimated deaths of these institutes was 30.76%. The percentage of obvious coding errors among deaths reported by county and above levels' medical institutes was as high as 22.87%. CONCLUSION: Network reporting system of death cases among county and above levels' medical institutes had remarkably increased the timeliness of data reporting system. Network reporting of data on death was the best opportunity to expand the coverage and to improve the quality of data reporting. Based on network reporting of death cases among county and above levels' medical institutes as well as deaths accrued at the communities should also be reported via this network in the eligible areas. The quality of coding on death causes among medical institutes were commonly poor, indicating that the training on ascertainment and coding of underlying death causes were quite essential.

China↗
PubMed2006

[Antitumor effects of nobiletin on Heps and its mechanism].

AIM: To study the inhibitory effect and mechanism of nobiletin on Heps tumor bearing mice. METHODS: Models of Heps tumor bearing mice were established. The inhibitory rates of tumor growth were calculated, the apoptosis morphology of tumor tissue was observed. The T lymphocyte transformation capacity was tested by MTT assay, the TNFalpha and IL-2 production were measured by LDH kits. RESULTS: Nobiletin could significantly inhibit Heps tumor growth. The inhibitory rates were 42.14% - 65.09% (P < 0.01). The morphology of tumor tissues in nobiletin group had typical characters of necrosis and apoptosis through transmission electron microscope. Nobiletin could stimulate T lymphocyte transformation and the production of TNFalpha and IL-2. CONCLUSION: Nobiletin has obvious antitumor effect on Heps, the main mechanism is to enhance the cellular immune function and induce apoptosis of tumor tissue.

Animals↗
PubMed2006

[Correlation of p73 polymorphisms to genetic susceptibilities to esophageal carcinoma and gastric cardiac carcinoma].

BACKGROUND & OBJECTIVE: p73 is a tumor suppressor gene. The two polymorphisms in the non-coding region of the exon 2 of p73 gene, named G4C14-A4T14, can form a stem-loop structure, and may influence p73 expression. This study was to investigate the correlation of p73 G4C14-A4T14 polymorphisms to susceptibilities to esophageal squamous cell carcinoma (ESCC) and gastric cardiac adenocarcinoma (GCA) in a high incidence region of Hebei Province. METHODS: We conducted a population-based case-control study in 348 ESCC patients, 259 GCA patients, and 630 healthy controls. p73 genotypes were determined by polymerase chain reaction-restrictive fragment length polymorphism (PCR-RFLP). RESULTS: Family history of upper gastrointestinal cancer (UGIC) significantly increased the risk of developing ESCC and GCA [the age, sex, and smoking status adjusted odds ratio (OR)=1.68, 95% confidence interval (CI)=1.28-2.20; OR=1.68, 95% CI=1.24-2.26, respectively]. The overall distribution of p73 genotype and allelotype in cancer patients and controls were not significantly different. Stratification analysis by smoking status and family history of UGIC found that the GC/AT genotype significantly increased the risk of developing GCA among the subjects without family history of UGIC (OR=1.71, 95% CI=1.14-2.57), while p73 G4C14-A4T14 polymorphisms did not increase the risk of developing ESCC and GCA in other subgroups. CONCLUSION: In p73 G4C14-A4T14 polymorphisms, the GC/AT genotype increases the risk of developing GCA among the subjects without family history of UGIC.

Adenocarcinoma↗
PubMed2005

Autophagy in chronically ischemic myocardium.

We tested the hypothesis that chronically ischemic (IS) myocardium induces autophagy, a cellular degradation process responsible for the turnover of unnecessary or dysfunctional organelles and cytoplasmic proteins, which could protect against the consequences of further ischemia. Chronically instrumented pigs were studied with repetitive myocardial ischemia produced by one, three, or six episodes of 90 min of coronary stenosis (30% reduction in baseline coronary flow followed by reperfusion every 12 h) with the non-IS region as control. In this model, wall thickening in the IS region was chronically depressed by approximately 37%. Using a nonbiased proteomic approach combining 2D gel electrophoresis with in-gel proteolysis, peptide mapping by MS, and sequence database searches for protein identification, we demonstrated increased expression of cathepsin D, a protein known to mediate autophagy. Additional autophagic proteins, cathepsin B, heat shock cognate protein Hsc73 (a key protein marker for chaperone-mediated autophagy), beclin 1 (a mammalian autophagy gene), and the processed form of microtubule-associated protein 1 light chain 3 (a marker for autophagosomes), were also increased. These changes, not evident after one episode, began to appear after two or three episodes and were most marked after six episodes of ischemia, when EM demonstrated autophagic vacuoles in chronically IS myocytes. Conversely, apoptosis, which was most marked after three episodes, decreased strikingly after six episodes, when autophagy had increased. Immunohistochemistry staining for cathepsin B was more intense in areas where apoptosis was absent. Thus, autophagy, triggered by ischemia, could be a homeostatic mechanism, by which apoptosis is inhibited and the deleterious effects of chronic ischemia are limited.

Animals↗
PubMed2005

Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis.

Although numerous fundamental aspects of development have been uncovered through the study of individual genes and proteins, system-level models are still missing for most developmental processes. The first two cell divisions of Caenorhabditis elegans embryogenesis constitute an ideal test bed for a system-level approach. Early embryogenesis, including processes such as cell division and establishment of cellular polarity, is readily amenable to large-scale functional analysis. A first step toward a system-level understanding is to provide 'first-draft' models both of the molecular assemblies involved and of the functional connections between them. Here we show that such models can be derived from an integrated gene/protein network generated from three different types of functional relationship: protein interaction, expression profiling similarity and phenotypic profiling similarity, as estimated from detailed early embryonic RNA interference phenotypes systematically recorded for hundreds of early embryogenesis genes. The topology of the integrated network suggests that C. elegans early embryogenesis is achieved through coordination of a limited set of molecular machines. We assessed the overall predictive value of such molecular machine models by dynamic localization of ten previously uncharacterized proteins within the living embryo.

Algorithms↗
PubMed2004

A map of the interactome network of the metazoan C. elegans.

To initiate studies on how protein-protein interaction (or "interactome") networks relate to multicellular functions, we have mapped a large fraction of the Caenorhabditis elegans interactome network. Starting with a subset of metazoan-specific proteins, more than 4000 interactions were identified from high-throughput, yeast two-hybrid (HT=Y2H) screens. Independent coaffinity purification assays experimentally validated the overall quality of this Y2H data set. Together with already described Y2H interactions and interologs predicted in silico, the current version of the Worm Interactome (WI5) map contains approximately 5500 interactions. Topological and biological features of this interactome network, as well as its integration with phenome and transcriptome data sets, lead to numerous biological hypotheses.

Animals↗
PubMed2004

Increasing specificity in high-throughput yeast two-hybrid experiments.

Since its inception, the yeast two-hybrid (Y2H) system has proven to be an efficient system to identify novel protein-protein interactions. However, Y2H screens are sometimes criticized for generating high rates of false-positives. Minimizing false-positive interactions is especially important in proteome wide high-throughput (HT) Y2H. Here, we summarize various approaches that reduce false-positives in HT-Y2H projects. We evaluated the potential of examining putative positives after removing the prey encoding plasmid by negative selection. We found that this method reliably identifies false-positives caused by spontaneous conversion of baits into auto-activators and provides significant time-savings in HT screens. In addition, we present a method to eliminate an important source of false-positives: contaminating prey plasmids. Y2H interactors can be wrongly identified due to the presence of two or more different plasmids in the cells of a single yeast colony. Of these independent plasmids, only one encodes a genuine interactor. Contaminating plasmids are eliminated by extended culture of yeast cells under positive selection for the interaction, allowing the identification of the true interaction partner.

Animals↗
PubMed2003

Integrating 'omic' information: a bridge between genomics and systems biology.

The availability of genome sequences for several organisms, including humans, and the resulting first-approximation lists of genes, have allowed a transition from molecular biology to 'modular biology'. In modular biology, biological processes of interest, or modules, are studied as complex systems of functionally interacting macromolecules. Functional genomic and proteomic ('omic') approaches can be helpful to accelerate the identification of the genes and gene products involved in particular modules, and to describe the functional relationships between them. However, the data emerging from individual omic approaches should be viewed with caution because of the occurrence of false-negative and false-positive results and because single annotations are not sufficient for an understanding of gene function. To increase the reliability of gene function annotation, multiple independent datasets need to be integrated. Here, we review the recent development of strategies for such integration and we argue that these will be important for a systems approach to modular biology.

Computational Biology↗
PubMed2002

Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline.

By integrating functional genomic and proteomic mapping approaches, biological hypotheses should be formulated with increasing levels of confidence. For example, yeast interactome and transcriptome data can be correlated in biologically meaningful ways. Here, we combine interactome mapping data generated for a multicellular organism with data from both large-scale phenotypic analysis ("phenome mapping") and transcriptome profiling. First, we generated a two-hybrid interactome map of the Caenorhabditis elegans germline by using 600 transcripts enriched in this tissue. We compared this map to a phenome map of the germline obtained by RNA interference (RNAi) and to a transcriptome map obtained by clustering worm genes across 553 expression profiling experiments. In this dataset, we find that essential proteins have a tendency to interact with each other, that pairs of genes encoding interacting proteins tend to exhibit similar expression profiles, and that, for approximately 24% of germline interactions, both partners show overlapping embryonic lethal or high incidence of males RNAi phenotypes and similar expression profiles. We propose that these interactions are most likely to be relevant to germline biology. Similar integration of interactome, phenome, and transcriptome data should be possible for other biological processes in the nematode and for other organisms, including humans.

Animals↗