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Jian-Min Chen

Publications and source records attributed to Jian-Min Chen.

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

LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease: mutation detection bias and multiple mechanisms of target gene disruption.

LINE-1 (L1) elements are the most abundant autonomous non-LTR retrotransposons in the human genome. Having recently performed a meta-analysis of L1 endonuclease-mediated retrotranspositional events causing human genetic disease, we have extended this study by focusing on two key issues, namely, mutation detection bias and the multiplicity of mechanisms of target gene disruption. Our analysis suggests that whereas an ascertainment bias may have generally militated against the detection of autosomal L1-mediated insertions, autosomal L1 direct insertions could have been disproportionately overlooked owing to their unusually large size. Our analysis has also indicated that the mechanisms underlying the functional disruption of target genes by L1-mediated retrotranspositional events are likely to be dependent on several different factors such as the type of insertion (L1 direct, L1 trans-driven Alu, or SVA), the precise locations of the inserted sequences within the target gene regions, the length of the inserted sequences, and possibly also their orientation.

Journal Article↗
PubMed2006

[Physical localization of ribosomal genes and chromosome DAPI banding by in situ hybridization in Medicago sativa L].

Physical localization of ribosomal genes in diploid and tetraploid alfalfa (Medicago. sativa) was studied using fluorescent in situ hybridization (FISH). It was revealed that 45s gene was only located at nucleolus organizer region (NOR) with a single locus in both diploid and tetraploid alfalfa, while 5s gene had 2-3 loci on chromosomes. Using the genomic DNA from M. coerulea and M. falcata as probe to hybridize with tetraploid species in alfalfa, both diploid species were successfully hybridized with tetraploid chromosomes, only showing the difference in hybridization signals in different numbers of chromosomes. Chromosomes of alfalfa exhibited DAPI banding by FISH analysis. In general, the patterns of distribution of DAPI banding were consistent with C-banding for M. coerulea. The possible origination of tetraploid alfalfa was discussed based on DAPI banding patterns and FISH analysis for ribosomal genes .

Chromosome Banding↗
PubMed2005

A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease.

Diverse long interspersed element-1 (LINE-1 or L1)-dependent mutational mechanisms have been extensively studied with respect to L1 and Alu elements engineered for retrotransposition in cultured cells and/or in genome-wide analyses. To what extent the in vitro studies can be held to accurately reflect in vivo events in the human genome, however, remains to be clarified. We have attempted to address this question by means of a systematic analysis of recent L1-mediated retrotranspositional events that have caused human genetic disease, with a view to providing a more complete picture of how L1-mediated retrotransposition impacts upon the architecture of the human genome. A total of 48 such mutations were identified, including those described as L1-mediated retrotransposons, as well as insertions reported to contain a poly(A) tail: 26 were L1 trans-driven Alu insertions, 15 were direct L1 insertions, four were L1 trans-driven SVA insertions, and three were associated with simple poly(A) insertions. The systematic study of these lesions, when combined with previous in vitro and genome-wide analyses, has strengthened several important conclusions regarding L1-mediated retrotransposition in humans: (a) approximately 25% of L1 insertions are associated with the 3' transduction of adjacent genomic sequences, (b) approximately 25% of the new L1 inserts are full-length, (c) poly(A) tail length correlates inversely with the age of the element, and (d) the length of target site duplication in vivo is rarely longer than 20 bp. Our analysis also suggests that some 10% of L1-mediated retrotranspositional events are associated with significant genomic deletions in humans. Finally, the identification of independent retrotranspositional events that have integrated at the same genomic locations provides new insight into the L1-mediated insertional process in humans.

Base Sequence↗
PubMed2005

Crystallographic determination of stereochemistry of biologically active 2'',3''-dibromo-7-epi-10-deacetylcephalomannine.

The stereochemistry at C2'' and C3'' of two diastereomers of 2'',3''-dibromo-7-epi-10-deacetylcephalomannine (6 and 7), which were synthesized by reacting 7-epi-10-deacetylcephalomannine (5) with bromine, were assigned unambiguously based on crystallographic studies of 6. The X-ray crystallographic analysis shows that 6 adopts an absolute configuration of (2''S,3''R), and 7 can be assigned as (2''R,3''S) configuration. The side-chain conformation of 6 was revealed to be different with the known hydrophobic collapse and the apolar conformations, as found in solid state and in solution. However, most side-chain torsion angles of 6 were found to be very similar to those of tubulin-bound T-shaped conformation (T-Taxol). Both 6 and 7 showed strong in vitro paclitaxel-like activity.

Antineoplastic Agents↗
PubMed2005

Meta-analysis of gross insertions causing human genetic disease: novel mutational mechanisms and the role of replication slippage.

Although gross insertions (>20 bp) comprise <1% of disease-causing mutations, they nevertheless represent an important category of pathological lesion. In an attempt to study these insertions in a systematic way, 158 gross insertions ranging in size between 21 bp and approximately 10 kb were identified using the Human Gene Mutation Database (www.hgmd.org). A careful meta-analytical study revealed extensive diversity in terms of the nature of the inserted DNA sequence and has provided new insights into the underlying mutational mechanisms. Some 70% of gross insertions were found to represent sequence duplications of different types (tandem, partial tandem, or complex). Although most of the tandem duplications were explicable by simple replication slippage, the three complex duplications appear to result from multiple slippage events. Some 11% of gross insertions were attributable to nonpolyglutamine repeat expansions (including octapeptide repeat expansions in the prion protein gene [PRNP] and polyalanine tract expansions) and evidence is presented to support the contention that these mutations are also caused by replication slippage rather than by unequal crossing over. Some 17% of gross insertions, all >or=276 bp in length, were found to be due to LINE-1 (L1) retrotransposition involving different types of element (L1 trans-driven Alu, L1 direct, and L1 trans-driven SVA). A second example of pathological mitochondrial-nuclear sequence transfer was identified in the USH1C gene but appears to arise via a novel mechanism, trans-replication slippage. Finally, evidence for another novel mechanism of human genetic disease, involving the possible capture of DNA oligonucleotides, is presented in the context of a 26-bp insertion into the ERCC6 gene.

Base Sequence↗
PubMed2005

Complex gene rearrangements caused by serial replication slippage.

The now-classical model of replication slippage can in principle account for both simple deletions and tandem duplications associated with short direct repeats. Invariably, a single replication slippage event is invoked, irrespective of whether simple deletions or tandem duplications are involved. However, we recently identified three complex duplicational insertions that could also be accounted for by a model of serial replication slippage. We postulate that a sizeable proportion of hitherto inexplicable complex gene rearrangements may be explained by such a model. To test this idea, and to assess the generality of our initial findings, a number of complex gene rearrangements were selected from the Human Gene Mutation Database (HGMD). Some 95% (20/21) of these mutations were found to be explicable by twin or multiple rounds of replication slippage, the sole exception being a double deletion in the F9 gene that is associated with DNA sequences that appear capable of adopting non-B conformations. Of the 20 complex gene rearrangements, 19 (seven simple double deletions, one triple deletion, two double mutational events comprising a simple deletion and a simple insertion, six simple indels that may constitute a novel and non-canonical class of gene conversion, and three complex indels) were compatible with the model of serial replication slippage in cis; the remaining indel in the MECP2 gene, however, appears to have arisen via interchromosomal replication slippage in trans. Our postulate that serial replication slippage may account for a variety of complex gene rearrangements has therefore received broad support from the study of the above diverse series of mutations.

Base Sequence↗
PubMed2005

Intrachromosomal serial replication slippage in trans gives rise to diverse genomic rearrangements involving inversions.

Serial replication slippage in cis (SRScis) provides a plausible explanation for many complex genomic rearrangements that underlie human genetic disease. This concept, taken together with the intra- and intermolecular strand switch models that account for mutations that arise via quasipalindrome correction, suggest that intrachromosomal SRS in trans (SRStrans) mediated by short inverted repeats may also give rise to a diverse series of complex genomic rearrangements. If this were to be so, such rearrangements would invariably generate inversions. To test this idea, we collated all informative mutations involving inversions of >or=5 bp but <1 kb by screening the Human Gene Mutation Database (HGMD; www.hgmd.org) and conducting an extensive literature search. Of the 21 resulting mutations, only two (both of which coincidentally contain untemplated additions) were found to be incompatible with the SRStrans model. Eighteen (one simple inversion, six inversions involving sequence replacement by upstream or downstream sequence, five inversions involving the partial reinsertion of removed sequence, and six inversions that occurred in a more complicated context) of the remaining 19 mutations were found to be consistent with either two steps of intrachromosomal SRStrans or a combination of replication slippage in cis plus intrachromosomal SRStrans. The remaining lesion, a 31-kb segmental duplication associated with a small inversion in the SLC3A1 gene, is explicable in terms of a modified SRS model that integrates the concept of "break-induced replication." This study therefore lends broad support to our postulate that intrachromosomal SRStrans can account for a variety of complex gene rearrangements that involve inversions.

Amino Acid Transport Systems, Basic↗
PubMed2005

Preparation and evaluation of new brominated paclitaxel analogues.

Two diastereomers of 2'',3''-dibromo-7-epi-10-deacetylcephalomannine, 4 and 5, have been synthesized, purified and identified for evaluation as antitumour drugs. The cytotoxicity of the two diastereomers, assessed in cell culture against MCF-7 breast cancer, A549 lung cancer and A2780 ovarian cancer, was slightly stronger than that of paclitaxel. The cytotoxicity of 5 outweighs that of 4. In the light of the difference in cytotoxicity between the two diastereomers, we can assume that the differing configurations of C-2'' and C-3'' of the two diastereomers may result in different bioactive conformations in solution and, consequently, different biologically relevant conformations for binding to tubulin/microtubules -- a matter we are studying further.

Antineoplastic Agents↗
PubMed2005

[Photooxidation of CS2 under ambient pressure and vacuum condition].

With the radiation of UV light, the photooxidation of CS2 was studied under ambient pressure and vacuum condition. By means of in-situ FTIR, XPS and GC-MS, it is confirmed that the products of the reaction are COS, SO2, CO and CO2. The reaction is apparent first-order. Under ambient pressure and vacuum condition the concentration of the intermediate product COS varies tremendously. Under ambient pressure the concentration of COS increases sharply and then decreases gently. While under vacuum condition COS rose only up to 1/10 that of the ambient pressure, and remained invariable until finally vanished slowly. Under ambient pressure and vacuum condition, the half life time of CS2 was 31.6 s and 39.8 s, and it took 55 min and 22 min to degrade 98% of COS respectively. Oxygen promotes CS2 photooxidation. The main products of the photooxidation of COS, which is an important intermediate of the photooxdiation of CS2, are CO2 and SO2. In addition, SO2 could be further oxidized into SO2(4-). Increasing appropriate amount of oxygen could promote the photooxidation activity of COS. However, the rate constant remains invariable when the oxygen is overloaded.

Air Pollutants↗
PubMed2005

[Recent advances in the determination methods of aflatoxins].

Aflatoxins are very harmful pollutants generally existing in peanuts, corns, farm products and so on. Many methods for the determination of aflatoxins have been developed in recent thirty years. The limits for aflatoxins have been set down for foods and farm products in different countries successively. In China, the methods for the determination of aflatoxins in foods cannot meet the need of new limit regulations. Aflatoxins were found in some traditional Chinese medicines according to some literatures. But the detective method and standard for the determination of aflatoxins is not established in active pharmacopoeia. The analytical methods for aflatoxins have been summarized in this paper, which can provide the references to the researchers who are engaged in the determination of aflatoxins in traditional Chinese medicines and foods. This paper mainly focuses on the liquid chromatography method with immunoaffinity column cleanup using post-column derivatization system for aflatoxins. Aflatoxins can be adsorbed in the immunoaffinity column peculiarly on the basis of this method, and then they can be eluted with organic solvent. It is the best way for cleanup using immunoaffinity column for the determination of aflatoxins in traditional Chinese medicines. This HPLC method with fluorescence detector using post-column derivatization system is a commonly used method in different countries, and it is more sensitive and accurate. Our studies have also proved that this method, that is: the liquid chromatography methods with immunoaffinity column cleanup using post-column derivatization system for aflatoxins, is the best method, which is suitable for the determination of aflatoxins in traditional Chinese medicines.

Aflatoxins↗
PubMed2004

Interaction between trypsinogen isoforms in genetically determined pancreatitis: mutation E79K in cationic trypsin (PRSS1) causes increased transactivation of anionic trypsinogen (PRSS2).

The human pancreas secretes two major trypsinogen isoforms, cationic and anionic trypsinogen. To date, 19 genetic variants have been identified in the cationic trypsinogen gene (PRSS1) of patients with hereditary, familial, or sporadic chronic pancreatitis. A common feature of cationic trypsinogen mutants studied so far is an increased propensity for autocatalytic activation (autoactivation). This is thought to lead to premature intrapancreatic digestive protease activation. In contrast, no pancreatitis-associated mutations have been found in the anionic trypsinogen gene (PRSS2), suggesting that this isoform might play a relatively unimportant role in pancreatitis. To challenge this notion, here we describe the unique properties of the E79K cationic trypsinogen mutation (c.235G>A), which was identified in three European families affected by sporadic or familial pancreatitis cases. In vitro analysis of recombinant wild-type and mutant enzymes revealed that catalytic activity of E79K trypsin was normal, and its inhibition by pancreatic secretory trypsin inhibitor was unaffected. Although the E79K mutation introduces a potential new tryptic cleavage site, autocatalytic degradation (autolysis) of E79K-trypsin was also unchanged. Furthermore, in contrast to previously characterized disease-causing mutations, E79K markedly inhibited autoactivation of cationic trypsinogen. Remarkably, however, E79K trypsin activated anionic trypsinogen two-fold better than wild-type cationic trypsin did, while the common pancreatitis-associated mutants R122H or N29I had no such effect. The observations not only suggest a novel mechanism of action for pancreatitis-associated trypsinogen mutations, but also highlight the importance of interactions between the two major trypsinogen isoforms in the development of genetically determined chronic pancreatitis.

Adult↗
PubMed2004

Genomic rearrangements in the CFTR gene: extensive allelic heterogeneity and diverse mutational mechanisms.

Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR/ABCC7). Despite the extensive and enduring efforts of many CF researchers over the past 14 years, up to 30% of disease alleles still remain to be identified in some populations. It has long been suggested that gross genomic rearrangements could account for these unidentified alleles. To date, however, only a few large deletions have been found in the CFTR gene and only three have been fully characterized. Here, we report the first systematic screening of the 27 exons of the CFTR gene for large genomic rearrangements, by means of the quantitative multiplex PCR of short fluorescent fragments (QMPSF). A well-characterized cohort of 39 classical CF patients carrying at least one unidentified allele (after extensive and complete screening of the CFTR gene by both denaturing gradient gel electrophoresis and denaturing high-performance liquid chromatography) participated in this study. Using QMPSF, some 16% of the previously unidentified CF mutant alleles were identified and characterized, including five novel mutations (one large deletion and four indels). The breakpoints of these five mutations were precisely determined, enabling us to explore the underlying mechanisms of mutagenesis. Although non-homologous recombination may be invoked to explain all five complex lesions, each mutation appears to have arisen through a different mechanism. One of the indels was highly unusual in that it involved the insertion of a short 41 bp sequence with partial homology to a retrotranspositionally-competent LINE-1 element. The insertion of this ultra-short LINE-1 element (dubbed a "hyphen element") may constitute a novel type of mutation associated with human genetic disease.

Alleles↗
PubMed2003

Evolution of trypsinogen activation peptides.

The activation peptide of mammalian trypsinogens contains a highly conserved tetra-aspartate sequence (D19-D20-D21-D22) preceding the K23-I24 scissile peptide bond, which is hydrolyzed as the first step in the activation process. Here, we examined the evolution and function of trypsinogen activation peptides through integrating functional characterization of disease-associated mutations with comparative genomic analysis. Activation properties of three chronic pancreatitis-associated activation peptide mutants (the novel D19A and the previously reported D22G and K23R) were simultaneously analyzed, for the first time, in the context of recombinant human cationic trypsinogen. A dramatic increase in autoactivation of cationic trypsinogen was observed in all three mutants, with D22G and K23R exhibiting the most marked increases. The physiological activator enteropeptidase activated the D19A mutant normally, activated the D22G mutant very poorly, and stimulated activation of the K23R mutant. The biochemical and structural data, taken together with a comprehensive sequence comparison, indicates that the tetra-aspartate sequence in mammalian trypsinogen activation peptides has evolved not only for optimal enteropeptidase recognition in the duodenum but also for efficient inhibition of trypsinogen autoactivation within the pancreas. Moreover, the use of lysine instead of arginine at the P1 position of activation peptides also has an advantageous effect against trypsinogen autoactivation. Finally, fixed substitutions in the key residues of the trypsinogen activation peptide may suggest the evolution of new functions unrelated to digestion, as found in the group III trypsinogens of cold-adapted fishes.

Amino Acid Sequence↗
PubMed2003

"Loss of function" mutations in the cationic trypsinogen gene (PRSS1) may act as a protective factor against pancreatitis.

Several genetic factors have been well known to predispose one to chronic pancreatitis (CP). However, little is known about the genetic factors that may provide a protective effect against the disease. Having found a nonsense mutation (c.111C>A; Y37X) and a splicing mutation (IVS2+1G>A) in the cationic trypsinogen gene (protease, serine, 1; PRSS1) in alcoholics without the development of CP, but not in alcoholics with CP and patients with hereditary or idiopathic CP, we propose that while "gain of function" mutations in the PRSS1 gene predispose one to pancreatitis, "loss of function" mutations in the gene may protect one against the disease.

Adult↗
PubMed2003

Trypsinogen hL is not a new member of the human trypsinogen family, but a known mouse ortholog.

An allegedly novel human trypsinogen cDNA clone termed trypsinogen hL was recently reported in the Biological & Pharmaceutical Bulletin (2003; 26: 361-364). This "new" trypsinogen sequence was isolated by PCR using human lung cDNAs as template and was presumed to be a new member of the human trypsinogen family. However, trypsinogen hL does not match any sequence in the human genome; whereas it is 100% identical to mouse trypsinogen 7. Thus, trypsinogen hL is not of human origin, and its cloning from a human cDNA library was clearly a result of contamination with mouse genetic material. Publication of this cloning artifact could have been avoided by a simple BLAST search of GenBank or other sequence databanks.

Animals↗
PubMed2003

Chromosomal location and expression of green fluorescent protein (gfp) gene in microspore derived transgenic barley (Hordeum vulgare L.).

Four doubled haploid barley lines (A, C, D, E) derived from gfp (green fluorescent protein) transformation and selection following particle bombardment of microspores were studied for gene expression pattern and the location of genome inserts. The integration sites were detected by fluorescence in situ hybridization (FISH) using the gfp plasmid DNA as a probe. Plants from events A, C, D and E all have a single insert site on chromosome 7L(5HL) at different locations while line E has a second insert site on chromosome 5S(7HS). All original transgenic plants were hemizygous for the transgenes and segregated in the T1 and T2 generations. Although line D had no GFP expression, FISH and PCR could detect gfp gene on its chromosome in transformed plants. Expression levels of GFP varied with lines and tissues examined. Plants from line C showed good expression in pollen and an intermediate level in root tips. Plants from A have intermediate expression of GFP in the pollen and light expression in the root tips. Line E showed strong expression in the root-tips and an intermediate level of GFP in the pollen. Lines A and C segregated as a single Mendelian locus while E segregated in a duplicate loci ratio (15:1) on seedling root tips but had low expression frequency in the pollen. PCR results were consistent with GFP expression on root tips in the three segregating lines. The expression of GFP for lines D and E was abnormal and may be related to the physical location of the transgene or the gene construct used.

Chromosome Mapping↗
PubMed2002

Inhibition of mitogen-activated protein kinase signaling by chloroquine.

Previously, we demonstrated that the anti-inflammatory drug chloroquine (CQ) inhibited LPS-induced TNF-alpha transcription. To define further the mechanism of CQ, we studied the effect of this drug on mitogen-activated protein kinase signaling pathways involved in regulation of TNF production. CQ interfered with phosphorylation of extracellular signal-regulated kinases (ERK)1/2 and the ERK-activating kinases mitogen-activating protein/ERK kinase (MEK)1/2. Both CQ and PD98059, a MEK1 inhibitor, reduced luciferase reporter activity driven by human TNF promoter sequences. However, CQ appeared to mediate these effects by deactivating Raf, the upstream activator of MEK. These findings were supported by functional data demonstrating that CQ and PD98059 interfered with TNF expression in several human and murine cell types while neither inhibitor blocked TNF production in murine RAW264.7 macrophages, a cell line that does not require MEK-ERK signaling for TNF production. Finally, we evaluated whether CQ could sensitize HeLa cells to undergo anti-Fas-mediated apoptosis, an effect observed when ERK activation is interrupted in this cell line. CQ rendered HeLa cells sensitive to anti-Fas treatment in a manner similar to PD98059. Taken together, these data argue that therapeutic concentrations of CQ interfere with ERK activation by a novel mechanism, an effect that could be responsible, at least in part, for the potent anti-inflammatory effects of this drug.

Animals↗