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Jianjun Chen

Publications and source records attributed to Jianjun Chen.

At least 37 records · Page 2Linked to original sources

Optimization under variability and uncertainty: a case study for NOx emissions control for a gasification system.

Methods for optimization of process technologies considering the distinction between variability and uncertainty are developed and applied to case studies of NOx control for Integrated Gasification Combined Cycle systems. Existing methods of stochastic optimization (SO) and stochastic programming (SP) are demonstrated. A comparison of SO and SP results provides the value of collecting additional information to reduce uncertainty. For example, an expected annual benefit of 240,000 dollars is estimated if uncertainty can be reduced before a final design is chosen. SO and SP are typically applied to uncertainty. However, when applied to variability, the benefit of dynamic process control is obtained. For example, an annual savings of 1 million dollars could be achieved if the system is adjusted to changes in process conditions. When variability and uncertainty are treated distinctively, a coupled stochastic optimization and programming method and a two-dimensional stochastic programming method are demonstrated via a case study. For the case study, the mean annual benefit of dynamic process control is estimated to be 700,000 dollars, with a 95% confidence range of 500,000 dollars to 940,000 dollars. These methods are expected to be of greatest utility for problems involving a large commitment of resources, for which small differences in designs can produce large cost savings.

Air Pollution↗

Over 20% of human transcripts might form sense-antisense pairs.

The major challenge to identifying natural sense- antisense (SA) transcripts from public databases is how to determine the correct orientation for an expressed sequence, especially an expressed sequence tag sequence. In this study, we established a set of very stringent criteria to identify the correct orientation of each human transcript. We used these orientation-reliable transcripts to create 26 741 transcription clusters in the human genome. Our analysis shows that 22% (5880) of the human transcription clusters form SA pairs, higher than any previous estimates. Our orientation-specific RT-PCR results along with the comparison of experimental data from previous studies confirm that our SA data set is reliable. This study not only demonstrates that our criteria for the prediction of SA transcripts are efficient, but also provides additional convincing data to support the view that antisense transcription is quite pervasive in the human genome. In-depth analyses show that SA transcripts have some significant differences compared with other types of transcripts, with regard to chromosomal distribution and Gene Ontology-annotated categories of physiological roles, functions and spatial localizations of gene products.

Base Pairing↗

Generation of longer 3' cDNA fragments from massively parallel signature sequencing tags.

Massively Parallel Signature Sequencing (MPSS) is a powerful technique for genome-wide gene expression analysis, which, similar to SAGE, relies on the production of short tags proximal to the 3'end of transcripts. A single MPSS experiment can generate over 10(7) tags, providing a 10-fold coverage of the transcripts expressed in a human cell. A significant fraction of MPSS tags cannot be assigned to known transcripts (orphan tags) and are likely to be derived from transcripts expressed at very low levels (approximately 1 copy per cell). In order to explore the potential of MPSS for the characterization of the human transcriptome, we have adapted the GLGI protocol (Generation of Longer cDNA fragments from SAGE tags for Gene Identification) to convert MPSS tags into their corresponding 3' cDNA fragments. GLGI-MPSS was applied to 83 orphan tags and 41 cDNA fragments were obtained. The analysis of these 41 fragments allowed the identification of novel transcripts, alternative tags generated from polymorphic and alternatively spliced transcripts, as well as the detection of artefactual MPSS tags. A systematic large-scale analysis of the genome by MPSS, in combination with the use of GLGI-MPSS protocol, will certainly provide a complementary approach to generate the complete catalog of human transcripts.

Alternative Splicing↗

Intraspecific responses in grain quality of 10 wheat cultivars to enhanced UV-B radiation under field conditions.

Field studies were conducted to determine the potential for intraspecific responses in grain quality of 10 wheat (Triticum aestivum) cultivars to enhanced ultraviolet-B (UV-B, 280-315 nm) radiation. The plants were exposed to 5 kJm(-2) supplemental UV-B radiation, simulating a depletion of 20% stratospheric ozone. In wheat cultivars tested, intraspecific responses in 16 amino acid contents and total amino acid contents in grains were found. Out of tested wheat cultivars, Dali 905, Mianyang 20, Wenmai 3, Chuxiong 8807 and Huining 18 showed significant increase in proteins, and Yunmai 39 and Huining 18 showed significant increase while Dali 905 and Chuxiong 8807 showed significant decrease in total sugar, respectively. No wheat cultivar showed significant change in rough starch content. Out of 10 cultivars 9 had a positive quality response index (QRI), while only Yunmai 39 showed negative response (QRI -1.19). According to QRI, the tolerance of 10 wheat cultivars to UV-B radiation had the following sequence, Huining 18>Mianyang 20>Mianyang 26>Wenmai 3>Dali 905>Longchun 16>Fengmai 24>Liaochun 9>Chuxiong 8807>Yunmai 39. Intraspecific responses in grain quality of 10 wheat cultivars to enhanced UV-B radiation existed under field conditions.

Amino Acids↗

Essential role of the voltage-dependent anion channel (VDAC) in mitochondrial permeability transition pore opening and cytochrome c release induced by arsenic trioxide.

The precise molecular mechanism underlying arsenic trioxide (As(2)O(3))-induced apoptosis is a subject of extensive study. Here, we show that clinically relevant doses of As(2)O(3) can induce typical apoptosis in IM-9, a multiple myeloma cell line, in a Bcl-2 inhibitable manner. We confirmed that As(2)O(3) directly induced cytochrome c (cyto c) release from isolated mouse liver mitochondria via the mitochondrial permeability transition pore, and we further identified the voltage-dependent anion channel (VDAC) as a biological target of As(2)O(3) responsible for eliciting cyto c release in apoptosis. First, pretreatment of the isolated mitochondria with an anti-VDAC antibody specifically prevented As(2)O(3)-induced cyto c release. Second, in proteoliposome experiments, VDAC by itself was sufficient to mediate As(2)O(3)-induced cyto c release, which could be specifically inhibited by Bcl-X(L). Third, As(2)O(3) induced mitochondria membrane potential (DeltaPsim) reduction and cyto c release only in the VDAC-expressing, but not in the VDAC-deficient yeast strain. Finally, we found that As(2)O(3) induced the increased expression and homodimerization of VDAC in IM-9 cells, but not in Bcl-2 overexpressing cells, suggesting that VDAC homodimerization could potentially determine its gating capacity to cyto c, and Bcl-2 blockage of VDAC homodimerization represents a novel mechanism for its inhibition of apoptosis.

Animals↗

SAGE is far more sensitive than EST for detecting low-abundance transcripts.

BACKGROUND: Isolation of low-abundance transcripts expressed in a genome remains a serious challenge in transcriptome studies. The sensitivity of the methods used for analysis has a direct impact on the efficiency of the detection. We compared the EST method and the SAGE method to determine which one is more sensitive and to what extent the sensitivity is great for the detection of low-abundance transcripts. RESULTS: Using the same low-abundance transcripts detected by both methods as the targeted sequences, we observed that the SAGE method is 26 times more sensitive than the EST method for the detection of low-abundance transcripts. CONCLUSIONS: The SAGE method is more efficient than the EST method in detecting the low-abundance transcripts.

3' Untranslated Regions↗

PRDX4, a member of the peroxiredoxin family, is fused to AML1 (RUNX1) in an acute myeloid leukemia patient with a t(X;21)(p22;q22).

The AML1 gene (also known as RUNX1) at 21q22 codes for core binding factor (CBF) alpha, which forms a heterodimer with CBF beta that acts as a transcriptional activating factor. CBF is a critical regulator in the generation and differentiation of definitive hematopoietic stem cells and is frequently disrupted in leukemia through chromosome translocations. We cloned a novel AML1 partner gene, PRDX4, in an X;21 translocation in a 74-year-old male patient diagnosed with acute myeloid leukemia-M2. Chromosome analysis detected a t(X;21)(p22;q22) as the sole abnormality in bone marrow samples. The involvement of AML1 was confirmed by fluorescence in situ hybridization studies. Using 3' RACE-PCR, we cloned a fusion between exon 5 of AML1 and exon 2 of PRDX4. RT-PCR confirmed the fusion and detected another fusion between exon 6 of AML1 and exon 2 of PRDX4, indicating alternative splicing of exon 6 of AML1 in the fusion transcripts. PRDX4 is one of six peroxiredoxin-family genes that are highly conserved in eukaryotes and prokaryotes and are ubiquitously expressed. Peroxiredoxin genes exhibit thioredoxin-dependent peroxidase activity and have been implicated in a number of other cellular functions such as cell proliferation and differentiation. PRDX4 plays a regulatory role in the activation of the transcription factor NF-kappaB and is significantly down-regulated in acute promyelocytic leukemia. This is the first example of antioxidant enzyme involvement in a chromosome translocation in leukemia.

Aged↗

Characterization of genomic breakpoints in MLL and CBP in leukemia patients with t(11;16).

The recurring chromosome translocation t(11;16)(q23;p13) is detected in leukemia patients, virtually all of whom have received previous chemotherapy with topoisomerase (topo) II inhibitors. In the t(11;16), 3' CBP, on 16p13, is fused to 5' MLL, on 11q23, resulting in an MLL-CBP fusion gene that plays an important role in leukemogenesis. In this study, we cloned genomic breakpoints of the MLL and CBP genes in the t(11;16) in the SN-1 cell line and in five patients with therapy-related leukemia, all of whom had received topo II inhibitors for previous tumors. In all patients except one, both the genomic MLL-CBP and the reciprocal fusions were cloned. Genomic breakpoints in MLL occurred in the 8.3-kb breakpoint cluster region in all patients, whereas the breakpoints in CBP clustered in an 8.2-kb region of intron 3 in four patients. Genomic breakpoints in MLL occurred in intron 11 near the topo II cleavage site in the SN-1 cell line and in one patient, and they were close to LINE repetitive sequences in two other patients. In the remaining two patients, genomic breakpoints were in intron 9 in Alu repeats. Genomic breakpoints in CBP occurred in and around Alu repeats in one and two patients, respectively. In two patients, the breaks were near LINE repetitive sequences, suggesting that repetitive DNA sequences may play a role. No specific recombination motifs were identified at or near the breakpoint junctions. No topo II cleavage sites were detected in introns 2 and 3 of CBP. However, there were deletions and duplications at the breakpoints in both MLL and CBP and microhomologies or nontemplated nucleotides at most of the genomic fusion junctions, suggesting that a nonhomologous end-joining repair mechanism was involved in the t(11;16).

Aged↗

Analysis of translocations that involve the NUP98 gene in patients with 11p15 chromosomal rearrangements.

The NUP98 gene has been reported to be fused with at least 15 partner genes in leukemias with 11p15 translocations. We report the results of screening of cases with cytogenetically documented rearrangements of 11p15 and the subsequent identification of involvement of NUP98 and its partner genes. We identified 49 samples from 46 hematology patients with 11p15 (including a few with 11p14) abnormalities, and using fluorescence in situ hybridization (FISH), we found that NUP98 was disrupted in 7 cases. With the use of gene-specific FISH probes, in 6 cases, we identified the partner genes, which were PRRX1 (PMX1; in 2 cases), HOXD13, RAP1GDS1, HOXC13, and TOP1. In the 3 cases for which RNA was available, RT-PCR was performed, which confirmed the FISH results and identified the location of the breakpoints in patient cDNA. Our data confirm the previous findings that NUP98 is a recurrent target in various types of leukemia.

Adolescent↗

Genetic relationships of Aglaonema species and cultivars inferred from AFLP markers.

BACKGROUND AND AIMS: Aglaonema is an important ornamental foliage plant genus, but genetic relationships among its species and cultivars have not been reported. This study analysed genetic relatedness of 54 cultivars derived from nine species using amplified fragment length polymorphism (AFLP) markers. METHODS: Initially, 48 EcoRI + 2/MseI + 3 primer set combinations were screened, from which six primer sets that showed clear scoreable and highly polymorphic fragments were selected and used for AFLP reactions. AFLP fragments were scored and entered into a binary data matrix as discrete variables. Jaccard's coefficient of similarity was calculated for all pair-wise comparisons among the 54 cultivars, and a dendrogram was constructed by the unweighted pair-group method using the arithmetic average (UPGMA). KEY RESULTS: The number of AFLP fragments generated per primer set ranged from 59 to 112 with fragment sizes varying from 50 to 565 bp. A total of 449 AFLP fragments was detected, of which 314 were polymorphic (70 %). All cultivars were clearly differentiated by their AFLP fingerprints. The 54 cultivars were divided into seven clusters; cultivars within each cluster generally share similar morphological characteristics. Cluster I contains 35 cultivars, most of them are interspecific hybrids developed mainly from A. commutatum, A. crispum or A. nitidum. However, Jaccard's similarity coefficients among these hybrids are 0.84 or higher, suggesting that these popular hybrid cultivars are genetically much closer than previously thought. This genetic similarity may imply that A. nitidum and A. crispum are likely progenitors of A. commutatum. CONCLUSIONS: Results of this study demonstrate the efficiency and ease of using AFLP markers for investigating genetic relationships of ornamental foliage plants, a group usually propagated vegetatively. The AFLP markers developed will help future Aglaonema cultivar identification, germplasm conservation and new cultivar development.

Araceae↗

[Innovation and practice of college educational system in otorhinolaryngology].

OBJECTIVE: A series of educational innovation was performed in order to resolve the difficulties and conflict in the education of otorhinolaryngology of medical college. METHOD: The college educational system of otorhinolaryngology was established and put in practice in four grades of medical undergraduate students of 1997-2000 grade. RESULT: The scores and ability of medical students in otorhinolaryngology are improved significantly. Educational supervisors and the managers give high appreciation to the educational innovation of otorhinolaryngology. It was demonstrated that the innovated educational system is satisfactory for the college education of otorhinolaryngology. CONCLUSION: The innovated college educational system of otorhinolaryngology afford a good way to solve the difficulties and conflict in the college education of otorhinolaryngology. It is also valuable to other subjects in the clinical medical education of college education system.

Education, Medical, Undergraduate↗

[Innovation of the curriculum system of otorhinolaryngology and its impact on education of capable medical students].

OBJECTIVE: The impact of the curriculum system innovation of otorhinolaryngology in the education of capable medical student was investigated. METHOD: The curriculum system of otorhinolaryngology in our college was innovated. The innovated curriculum of otorhinolaryngology was put in practice in 3 grades of undergraduate students and 2 grades of seven-year education system students. RESULT: The clinical practice ability and the mast of the knowledge of otorhinolaryngology were improved significantly. CONCLUSION: The principle of the curriculum system innovation of otorhinolaryngology in our college is effective and, therefore, valuable in education of potential and capable medical students for other subjects of clinical medicine.

Curriculum↗

[Clinical therapic procedure of obstinate epistaxis].

OBJECTIVE: To investigate the clinical treatment consideration and the therapic procedure. METHOD: We analyze the clinical data of 171 cases of obstinate epistaxis in recent years, mainly the pathogeny, treatment consideration and therapic procedure. RESULT: Were two steps were selected to the therapeutics according to different causations: step one, using the methods including nasal septum rectification, nasal cavity microwave cauterization, the curative ratio were 87.20%, 91.25% respectively; step two, using the methods including DSA (digital subtraction angiography), ligation of the external carotid artery, arteria ethmoidalis clipping, the curative ratio were 90%, 100%, 100% respectively. CONCLUSION: The thought of taking two steps methods to treat the obstinate epistaxis is very clear, and the curative effect is satisfactory as well.

Adolescent↗

Identification of the protein-protein contact site and interaction mode of human VDAC1 with Bcl-2 family proteins.

Bcl-2 family of proteins plays differential roles in regulation of mitochondria-mediated apoptosis, by either promoting or inhibiting the release of apoptogenic molecules from mitochondria to cytosol. Bcl-2 family proteins modulate the mitochondrial permeability through interaction with adenine nucleotide translocator (ANT), voltage-dependent anion channel (VDAC), ADP/ATP exchange, or oxidative phosphorylation during apoptosis. Although the mitochondrial homeostasis is affected by the relative ratio of pro- and anti-apoptotic Bcl-2 family members, the molecular mechanism underlying the release of mitochondrial intermembrane proteins remains elusive. Here we reported the biochemical evidence that both pro-apoptotic Bax and anti-apoptotic Bcl-X(L) might simultaneously contact the putative loop regions of human VDAC1, and the existence of VDAC1-Bax-Bcl-X(L) tertiary complex in vitro suggested that VDAC1 channel conformation and mitochondrial permeability could be determined by the delicate balance between Bax and Bcl-X(L).

Binding Sites↗

Duplexes of 21-nucleotide RNAs mediate RNA interference in differentiated mouse ES cells.

RNA interference (RNAi) is a novel phenomenon that can induce post-transcriptional gene silencing (PTGS) both in animals and plants. RNAi is effective in suppressing specific gene expression in the early mouse embryonic cells and in undifferentiated embryonic stem (ES) cells. In this study, we demonstrate that dsRNA is effective in inducing PTGS in differentiated ES cells: CD34+ embryoid body (EB) cells, as confirmed by western blot and immunocytochemical staining. PU.1 is a key transcription factor in myeloid differentiation. Undifferentiated ES cells do not express PU.1; however it is expressed when ES cells differentiate into EBs. PU.1 could be suppressed by the specific PU.1 dsRNA, but not non-specific Lamin A/C dsRNA, in the CD34+ EB cells when they were induced to myeloid differentiation in the presence of GM-CSF and IL-3. As a consequence, the level of expression of CD115 (M-CSF receptor), one of the downstream genes regulated by PU.1 is decreased in PU.1 dsRNA treated CD34+ EB cells, but not in Lamin A/C dsRNA treated cells. To explore this phenomenon in other myeloid gene, we also found that C/EBPalpha gene could be knocked down by C/EBPalpha dsRNA. Our finding demonstrates that RNAi is effective in inhibiting specific gene expression in differentiated ES cells. RNAi offers a new methodology for study of hematopoietic regulation using ES cell differentiation.

Animals↗

[Relationship between Dermatophagoides pteronyssinus and Dermatophagoides farinae sIgE in serum and local secretion of perennial allergic rhinitis patients].

OBJECTIVE: To investigate the relationship between Dermatophagoides pteronyssinus(Dp) and Dermatophagoides farinae(Df) specific IgE in the serum or local secretion of perennial allergic rhinitis (PAR) patients. METHOD: The serum and nasal secretion of suspected PAR patients were collected, then the concentration of mite sIgE in them were measured and analyzed. RESULT: The concentration of Dp and Df in serum or the local secretion was almost the same. The relationship between the two mite sIgE concentration and logarithm is good both in the serum or the local secretion(relative coefficient is about 0.97). CONCLUSION: The sIgE amount of the two mite is very similar in the body of the suspected AR patients, so only one kind of sIgE is needed to be measured to reflect the allergic situation in clinic.

Adolescent↗

[Factors influencing phosphorus loss by runoff process from farmlands in the dianchi watershed].

By laboratory simulated experiment, the effects of soil factors on the farmland phosphorus losses and its concentration were studied under artificial rainfall and nature rainfall. A number of soil and landscape factors were taken into account such as slopeness, soil and plant covers, fertilizers and application performances as well as rainfall intensity. The study showed that the concentration of total phosphorus (TP) and the loss rate varied with slopeness, being highest at slopness of 18 degrees with the values of 0.138 mg.L-1 and 6.14 kg.hm-2. There was no significant difference in TP concentration and the loss rate between under artificial rainfall and under nature rainfall. Moreover, TP concentration in runoff was smaller with the courser soil surface texture, and obviously lower with crop covering than without covering, among which the loss decreased 0.9-2.8 kg.hm-2 at different level of slope. Fertilizer application remarkably enchanced TP concentration and, thus, total phosphorus loss by runoff.

Crops, Agricultural↗

[Expression of NO and NOS in nasal polyps].

OBJECTIVE: To investigate the expression of nitric oxide synthase(NOS) in nasal polyps tissue and also to study the function of nitric oxide in the pathology of nasal polyps. METHOD: Investigating the expression of iNOS, eNOS with immunohistochemical staining, and the expression of iNOS mRNA with hybridization in situ. Analysing the production of nitric oxide in the nasal polyps through nitrate reductase technique. RESULT: In the polyps group, eNOS located in gland cells, epithelial and vascular endothelial cells, the staining of which was a little stronger than those of controls. The staining of iNOS was fairly strong in the epithelial cells, and it expressed mostly in the inflammatory cells inside the tissue. CONCLUSION: eNOS may play a role in glandular secretion and vascular dilatation. The increase of eNOS might respond to the enhanced nasal secretion and edema of nasal mocusa. Large amount of NO produced by iNOS may deteriorate the inflammation process of nasal polyps.

Adult↗