Biomedical subjects

F Liang

Publications and source records attributed to F Liang.

At least 37 records · Page 2Linked to original sources

PubMed2000

Anchoring of rice BAC clones to the rice genetic map in silico.

A wealth of molecular resources have been developed for rice genomics, including dense genetic maps, expressed sequence tags (ESTs), yeast artificial chromosome maps, bacterial artificial chromosome (BAC) libraries and BAC end sequence databases. Integration of genetic and physical maps involves labor-intensive empirical experiments. To accelerate the integration of the bacterial clone resources with the genetic map for the International Rice Genome Sequencing Project, we cleaned and filtered the available EST and BAC end sequences for repetitive sequences and then searched all available rice genetic markers with our filtered databases. We identified 418 genetic markers that aligned with at least one BAC end sequence with >95% sequence identity, providing a set of large insert clones with an average separation of 1 Mb that can serve as nucleation points for the sequencing phase of the International Rice Genome Sequencing Project.

Chromosome Mapping↗

PubMed2000

An optimized protocol for analysis of EST sequences.

The vast body of Expressed Sequence Tag (EST) data in the public databases provide an important resource for comparative and functional genomics studies and an invaluable tool for the annotation of genomic sequences. We have developed a rigorous protocol for reconstructing the sequences of transcribed genes from EST and gene sequence fragments. A key element in developing this protocol has been the evaluation of a number of sequence assembly programs to determine which most faithfully reproduce transcript sequences from EST data. The TIGR Gene Indices constructed using this protocol for human, mouse, rat and a variety of other plant and animal models have demonstrated their utility in a variety of applications and are freely available to the scientific research community.

Algorithms↗

PubMed2000

Integrin dependence of brain natriuretic peptide gene promoter activation by mechanical strain.

Expression of the brain natriuretic peptide (BNP) gene in cultured neonatal rat ventricular myocytes is activated by mechanical strain in vitro. We explored the role of cell-matrix contacts in initiating the strain-dependent increment in human BNP (hBNP) promoter activity. Coating the culture surface with fibronectin effected a dose-dependent increase in basal hBNP luciferase activity and amplification of the response to strain. Preincubation of myocytes with an RGD peptide (GRGDSP) or with soluble fibronectin, each of which would be predicted to compete for cell-matrix interactions, resulted in a dose-dependent reduction in strain-dependent hBNP promoter activity. A functionally inert RGE peptide (GRGESP) was without effect. Using fluorescence-activated cell sorting, we demonstrated the presence of beta(1), beta(3), and alpha(v)beta(5) integrins in myocytes as well as non-myocytes and alpha1 only in non-myocytes in our cultures. Inclusion of antibodies directed against beta(1), beta(3), or alpha(v)beta(5), but not alpha(1), alpha(2), or cadherin, was effective in blocking the BNP promoter response to mechanical strain. These same antibodies (anti-beta(3), -beta(1), and -alpha(v)beta(5)) had a similar inhibitory effect on strain-stimulated ERK, p38 MAPK, and, to a lesser extent, JNK activities in these cells. Cotransfection with chimeric integrin receptors capable of acting as dominant-negative inhibitors of integrin function demonstrated suppression of strain-dependent BNP promoter activity when vectors encoding beta(1) or beta(3), but not beta(5), alpha(5), or a carboxyl-terminal deletion mutant of beta(3) (beta(3)B), were employed. These studies underscore the importance of cell-matrix interactions in controlling cardiac gene expression and suggest a potentially important role for these interactions in signaling responses to mechanical stimuli within the myocardium.

Animals↗

PubMed2000

Immunohistochemical examination of the lungs in infant death cases using antibodies against milk components.

To examine the use of immunohistochemical staining with antibodies against milk components for detection of aspirated milk on lung sections, eighteen infant death cases were investigated. Immunostaining was performed with anti-human alpha lactalbumin, anti-human IgA, anti-human milk fat globulin 1, and anti-cow whey antibody. Reactivity with each antibody was examined, and semi-quantitative examinations were performed to compare the amount of aspirated milk using anti-human alpha lactalbumin antibody. Materials in the alveoli or bronchioli on lung sections suspected to be aspirated milk showed the most sensitive and clearest reaction with anti-human alpha lactalbumin antibody. Of the eighteen cases, ten cases showed positive reaction with this antibody. The amount of aspirated milk varied widely in each case. In conclusion, immunohistochemical staining with antibodies against human milk components, especially anti-human alpha lactalbumin antibody, can detect small amounts of milk. Using this method, we were able to compare the relative amount of aspirated milk among cases.

Analysis of Variance↗

PubMed2000

Differential expression of gamma-aminobutyric acid type B receptor-1a and -1b mRNA variants in GABA and non-GABAergic neurons of the rat brain.

To understand the heterogeneity of gamma-aminobutyric acid type B receptor (GABABR)-mediated events, we investigated expression of GABABR1a and 1b mRNA variants in GABA and non-GABAergic neurons of the rat central nervous system (CNS), by using nonradioactive in situ hybridization histochemistry and, in combination with GABA immunocytochemistry, double labeling. In situ hybridization with a pan probe, which recognizes a common sequence of both GABABR1a and GABABR1b mRNA variants, demonstrated widespread expression of GABABR1 mRNA at various levels in the CNS. Both GABABR1a and GABABR1b were expressed in the neocortex, hippocampus, dorsal thalamus, habenula, and septum, but only GABABR1a was detected in cerebellar granule cells, in caudate putamen, and most hindbrain structures. A majority of GABA neurons in cerebral cortex showed hybridization signals for both GABABR1a and GABABR1b, whereas those in most subcortical structures expressed either or neither of the two. GABA neurons in thalamic reticular nucleus and caudate putamen hybridized primarily for GABABR1a. Purkinje cells in the cerebellar cortex expressed predominantly GABABR1b. GABA neurons in dorsal lateral geniculate nucleus did not display significant levels of either GABABR1a or GABABR1b mRNAs. These data suggested widespread availability of GABABR-mediated inhibition in the CNS. The differential but overlapping expression of GABABR1 mRNA variants in different neurons and brain structures may contribute to the heterogeneity of GABABR-mediated inhibition. Some GABA neurons possessed, but others might lack the molecular machinery for GABABR-mediated disinhibition, autoinhibition, or both.

Animals↗

PubMed2000

The TIGR gene indices: reconstruction and representation of expressed gene sequences.

Expressed sequence tags (ESTs) have provided a first glimpse of the collection of transcribed sequences in a variety of organisms. However, a careful analysis of this sequence data can provide significant additional functional, structural and evolutionary information. Our analysis of the public EST sequences, available through the TIGR Gene Indices (TGI; http://www.tigr.org/tdb/tdb.html ), is an attempt to identify the genes represented by that data and to provide additional information regarding those genes. Gene Indices are constructed for selected organisms by first clustering, then assembling EST and annotated gene sequences from GenBank. This process produces a set of unique, high-fidelity virtual transcripts, or tentative consensus (TC) sequences. The TC sequences can be used to provide putative genes with functional annotation, to link the transcripts to mapping and genomic sequence data, and to provide links between orthologous and paralogous genes.

Base Sequence↗

PubMed2000

Gene index analysis of the human genome estimates approximately 120,000 genes.

Although sequencing of the human genome will soon be completed, gene identification and annotation remains a challenge. Early estimates suggested that there might be 60,000-100,000 (ref. 1) human genes, but recent analyses of the available data from EST sequencing projects have estimated as few as 45,000 (ref. 2) or as many as 140, 000 (ref. 3) distinct genes. The Chromosome 22 Sequencing Consortium estimated a minimum of 45,000 genes based on their annotation of the complete chromosome, although their data suggests there may be additional genes. The nearly 2,000,000 human ESTs in dbEST provide an important resource for gene identification and genome annotation, but these single-pass sequences must be carefully analysed to remove contaminating sequences, including those from genomic DNA, spurious transcription, and vector and bacterial sequences. We have developed a highly refined and rigorously tested protocol for cleaning, clustering and assembling EST sequences to produce high-fidelity consensus sequences for the represented genes (F.L. et al., manuscript submitted) and used this to create the TIGR Gene Indices-databases of expressed genes for human, mouse, rat and other species (http://www.tigr.org/tdb/tgi.html). Using highly refined and tested algorithms for EST analysis, we have arrived at two independent estimates indicating the human genome contains approximately 120,000 genes.

Algorithms↗

PubMed2000

Calmodulin activation of an endoplasmic reticulum-located calcium pump involves an interaction with the N-terminal autoinhibitory domain.

To investigate how calmodulin regulates a unique subfamily of Ca(2+) pumps found in plants, we examined the kinetic properties of isoform ACA2 identified in Arabidopsis. A recombinant ACA2 was expressed in a yeast K616 mutant deficient in two endogenous Ca(2+) pumps. Orthovanadate-sensitive (45)Ca(2+) transport into vesicles isolated from transformants demonstrated that ACA2 is a Ca(2+) pump. Ca(2+) pumping by the full-length protein (ACA2-1) was 4- to 10-fold lower than that of the N-terminal truncated ACA2-2 (Delta2-80), indicating that the N-terminal domain normally acts to inhibit the pump. An inhibitory sequence (IC(50) = 4 microM) was localized to a region within valine-20 to leucine-44, because a peptide corresponding to this sequence lowered the V(max) and increased the K(m) for Ca(2+) of the constitutively active ACA2-2 to values comparable to the full-length pump. The peptide also blocked the activity (IC(50) = 7 microM) of a Ca(2+) pump (AtECA1) belonging to a second family of Ca(2+) pumps. This inhibitory sequence appears to overlap with a calmodulin-binding site in ACA2, previously mapped between aspartate-19 and arginine-36 (J.F. Harper, B. Hong, I. Hwang, H.Q. Guo, R. Stoddard, J.F. Huang, M.G. Palmgren, H. Sze ¿1998 J Biol Chem 273: 1099-1106). These results support a model in which the pump is kept "unactivated" by an intramolecular interaction between an autoinhibitory sequence located between residues 20 and 44 and a site in the Ca(2+) pump core that is highly conserved between different Ca(2+) pump families. Results further support a model in which activation occurs as a result of Ca(2+)-induced binding of calmodulin to a site overlapping or immediately adjacent to the autoinhibitory sequence.

Calcium↗

PubMed2000

Diversity and regulation of plant Ca2+ pumps: insights from expression in yeast.

The spatial and temporal regulation of calcium concentration in plant cells depends on the coordinate activities of channels and active transporters located on different organelles and membranes. Several Ca2+ pumps have been identified and characterized by functional expression of plant genes in a yeast mutant (K616). This expression system has opened the way to a genetic and biochemical characterization of the regulatory and catalytic features of diverse Ca2+ pumps. Plant Ca(2+)-ATPases fall into two major types: AtECA1 represents one of four or more members of the type IIA (ER-type) Ca(2+)-ATPases in Arabidopsis, and AtACA2 is one of seven or more members of the type IIB (PM-type) Ca(2+)-ATPases that are regulated by a novel amino terminal domain. Type IIB pumps are widely distributed on membranes, including the PM (plasma membrane), vacuole, and ER (endoplasmic reticulum). The regulatory domain serves multiple functions, including autoinhibition, calmodulin binding, and sites for modification by phosphorylation. This domain, however, is considerably diverse among several type IIB ATPases, suggesting that the pumps are differentially regulated. Understanding of Ca2+ transporters at the molecular level is providing insights into their roles in signaling networks and in regulating fundamental processes of cell biology.

Arabidopsis↗

PubMed2000

Endothelin-dependent and -independent components of strain-activated brain natriuretic peptide gene transcription require extracellular signal regulated kinase and p38 mitogen-activated protein kinase.

The application of mechanical strain to cultured cardiac myocytes in vitro leads to activation of the brain natriuretic peptide (BNP) gene promoter, a marker of cardiac hypertrophy. We have previously shown that this activation results from both a direct mechanostimulatory event and an indirect autocrine/paracrine stimulation involving the sequential production of angiotensin II and endothelin (ET). In the present study, we examined the role of p38 mitogen-activated protein kinase (MAPK) and extracellular signal regulated kinase (ERK) in signaling the increase in promoter activity trafficking through each of these pathways. ET was shown to stimulate both p38 MAPK and ERK activity in these cultures and to activate human BNP (hBNP) promoter activity. Activation of the promoter was inhibited approximately 45% by SB-203580, a p38 MAPK inhibitor, and approximately 70% by PD98059, an inhibitor of the ERK-activating kinase MAPK kinase. The ET-independent (ie, direct) stimulation of the hBNP promoter by mechanical strain was inhibited approximately 70% by SB-203580 and approximately 60% by PD98059, implying that similar signaling circuitry is used, albeit to different degrees, by the direct and indirect pathways. The p38 MAPK component of both the ET-dependent and the ET-independent responses to strain appears to operate through a series of nuclear factor-kappaB binding, shear stress response element-like structures in the hBNP gene promoter. Collectively, these data suggest that activation of the BNP promoter by hypertrophic stimuli involves the participation of several independent signaling pathways. Such redundancy would help to guarantee generation of the full hypertrophic phenotype independently of the nature of the hypertrophic stimulus.

Animals↗

PubMed2000

[Endoluminal stent-graft repair of aortic aneurysms].

OBJECTIVE: To study the clinical value of the treatment of aortic aneurysms with endovascular stent-graft prosthesis. METHODS: After a unilateral surgical arteriotomy, Talent, Vanguard and Chinese stent-graft were advanced through the femoral arteries and placed in the proper position of the aneurysm sac under X-ray fluoroscopic guidance. RESULTS: Four patients with descending aneurysm, 1 patient with abdominal aortic aneurysm (AAA) involving the renal artery, superior mesenteric artery and celiac artery, and 1 patient with right common iliac artery aneurysm received straight stent-grafts. Five patients with infrarenal AAA received bifurcated stent-grafts. CT and MRA were performed during a follow-up of 3 - 19 months. Aortic aneurysms were completely excluded from the circulation. Five patients prolonged fever was noted and 1 patient was found to have a leakage 3 months later, and hemiplegia in 1 after procedure. CONCLUSIONS: Endovascular treatment of aortic aneurysm is technically feasible and can effectively exclude aortic aneurysms from the circulation. Endoluminal repair may serve as an interventional strategy to treat aneurysm, especially in patients at high surgical risk, but long term effect needs further study.

Adult↗

PubMed2000

[Abdominal aortic aneurysm treated by endovascular stent-graft and conventional surgical repair: a comparison].

OBJECTIVE: To evaluate the feasibility of abdominal aortic aneurysm (AAA) treated by endovascular stent-graft. METHODS: The clinical data of 52 patients with AAA treated by endovascular stent-graft (n = 20) and conventional surgical repair (n = 32) were analysed retrospectively. Patients conditions, operative hours, blood loss, function recovery and complications were compared. RESULTS: No significant difference was observed in sex, age, other disease, anesthesia risk category, aneurysm type, aneurysm diameter, technical success rate, and mortality rate between the groups (P > 0.05). The patients who underwent intraluminal treatment had significant reductions in operative time, blood loss, intensive care unit and hospitalization. But there was a high complication rate in the endovascular stent-graft group. All complications were connected with the interventional technique; endo-leak was the chief complication after operation. CONCLUSIONS: Endovascular treatment has marked merits such as reduced trauma, short hospitalization stays, and early functional recovery. It is suitable for the patients who can't undergo open surgical repair. But the complications caused by this technique needs further study.

Aged↗

PubMed2000

[The survey of HIV prevalence among drug users in Guangxi, China].

OBJECTIVE: To understand the distribution and related risk factors of HIV infection among drug users in Guangxi. METHOD: Three hundred and twenty five drug users were tested for serum HIV antibody, with enzyme linked immunosorbent assay. RESULTS: One hundred and sixteen drug users (35.7%) were found to be HIV positive. The main risk factors associated with HIV infection were intravenous drug users and needle sharing among drug users. The HIV prevalence was 40.9% (114/279) among IDUs, and only 4.3% (2/46) among oral drug users. The phenomenon of sharing injecting equipment (76.7%) among intravenous drug users in Guangxi represents a very serious problem. CONCLUSION: There is a high risk of HIV infection among drug users in Guangxi. Prevention programs urgently need to be implemented.

Adolescent↗

PubMed2000

[Study on the packings of affinity chromatography for the separation of urokinase].

Two kinds of affinity chromatographic packings for the separation of urokinase were synthesized by coupling of p-amino benzamidine (p-ABZ) to commercially available sepharose and polyepoxypropyl methacrylate (PEPMA). Then they were applied for separating crude urokinase. It was found that the average recovery of bioactivity on sepharose was higher than that on PEPMA, resulting in 108.3% and 43.4% respectively. The high rigidity of PEPMA permits fast flow of protein solutions and operation by higher-pressure affinity chromatography. The average purification times were 36.9 folds for PEPMA column and nine-folds for Sepharose column. The purification of crude urokinase described in this paper demonstrates that PEPMA column is effective for purifying biological products in a large scale.

Chromatography, Affinity↗

PubMed1999

The processing of secretogranin II in the peripheral nervous system: release of secretoneurin from porcine sympathetic nerve terminals.

The distribution of secretoneurin (SN), a peptide derived from secretogranin II (SgII), in the coeliac ganglion, the splenic nerve and the spleen was examined by immunohistochemistry. In the ganglion, SN immunoreactivity (IR) was unevenly distributed. Positive nerve terminals densely surrounded some postganglionic perikarya in which also intense SN-IR was present. In the crushed splenic nerves, intense immunoreactivities appeared proximal (but to a less extent also distal) to the crush of the nerve. Analysis by cytofluorimetric scanning (CFS) demonstrated that SN-IR and neuropeptide Y immunoreactivity (NPY-IR) were predominant in the axons proximal to the crush representing anterogradely transported components. Using radioimmunoassay (RIA) we demonstrated that upon electrical stimulation (10 Hz, 1 min) of the splenic nerve, significant amounts of SN-IR (64.2+/-2.3 fmol) were released together with NA (4. 1x106+/-0.2 fmol) and NPY (330.0+/-7.2 fmol) from the isolated perfused porcine spleen. To evaluate the processing of SgII in sympathetic neurons, boiled tissue extracts (coeliac ganglia and splenic nerve) and boiled spleen perfusate (used as a suitable source for vesicle derived peptides) were analysed by gel filtration chromatography followed by SN-RIA. In all cases immunoreactivity was present solely as SN, indicating that SgII was fully processed to the free peptide. The evidence that SN is transported to the nerve terminals and is released from the porcine spleen upon nerve stimulation, suggests that it may modulate adrenergic neurotransmission and may also play a role in the neuroimmune communication.

Animals↗

PubMed1999

Three-dimensional analysis of the 16 nm urothelial plaque particle: luminal surface exposure, preferential head-to-head interaction, and hinge formation.

The luminal surface of mouse urothelium in contact with the urine is almost entirely covered with plaques consisting of uroplakin-containing particles that form p6 hexagonal crystals with a center-to-center distance of 16 nm. A combination of quick-freeze/deep-etch images and our previous negative staining data indicate that the head domain of the uroplakin particle, which is exposed without an extensive glycocalyx shield, interacts closely with the head domains of the neighboring particles, while the membrane-embedded tail domains are farther apart; and that urothelial particles and plaques are not rigid structures as they can change their configuration in response to mechanical perturbations. Based on these data, we have constructed three-dimensional models depicting the structural organization of urothelial particles and plaques. Our models suggest that the head-to-head interaction may play a key role in determining the shape and size of the urothelial plaques. These models can explain many properties of urothelial plaques including their unique shape, detergent-insolubility, and morphological changes during vesicle maturation.

Animals↗

PubMed1999

Pig splenic nerve: peptides derived from chromogranins by proteolytic processing during axonal transport.

We have investigated the proteolytic processing of chromogranin A, chromogranin B and NESP55 (a novel chromogranin-like protein) during axonal transport using pig splenic nerve as a model. We have also studied the presence of chromogranin-derived peptides in the perfusate during electrical stimulation of this nerve. High-performance gel filtration chromatography followed by radioimmunoassay (RIA) revealed that chromogranins are proteolytically processed to varying degrees during axonal transport. For chromogranin A and NESP55, the precursor is still present in the proximal part of the nerve, whereas in the distal part and nerve terminals, intermediate-sized peptides and the free peptides GE-25 and GAIPIRRH dominate, respectively. For chromogranin B, the precursor has already been processed to an intermediate-sized peptide in the proximal part of the nerve, which is also present in the distal parts together with the free peptide PE-11. For chromogranin B and NESP55, only the free peptides PE-11 and GAIPIRRH, or in the case of chromogranin A, the free peptide GE-25 plus an intermediate-sized one, are released from the terminals into the splenic perfusate. These results demonstrate that chromogranins are processed to smaller peptides during axonal transport.

Animals↗

PubMed1999

Urothelial hinge as a highly specialized membrane: detergent-insolubility, urohingin association, and in vitro formation.

Urothelial surface is covered by numerous plaques (consisting of asymmetric unit membranes or AUM) that are interconnected by ordinary looking hinge membranes. We describe an improved method for purifying bovine urothelial plaques using 2% sarkosyl and 25 mM NaOH to remove contaminating membrane and peripheral proteins selectively. Highly purified plaques interconnected by intact hinge areas were obtained, indicating that the hinges are as detergent-insoluble as the plaques. These plaque/hinge preparations contained uroplakins, an as yet uncharacterized 18-kDa plaque-associated protein, plus an 85-kDa glycoprotein that is known to be hinge-associated in situ. Examination of the isolated, in vitro-resealed bovine AUM vesicles by quick-freeze deep-etch showed that each AUM particle consists of a 16-nm, luminally exposed "head" anchored to the lipid bilayer via a 9-mm transmembranous "tail", and that an AUM plaque can break forming several smaller plaques separated by newly formed particle-free, hinge-like areas. These data lend support to our recently proposed three-dimensional model of mouse urothelial plaques. In addition, our findings suggest that urothelial plaques are dynamic structures that can rearrange giving rise to new plaques with intervening hinges; that the entire urothelial apical surface (both plaque and hinge areas) is highly specialized; and that these two membrane domains may be equally important in fulfilling some of the urothelial functions.

Animals↗