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Biomedical subjects

Yi Zhao

Publications and source records attributed to Yi Zhao.

At least 37 records · Page 2Linked to original sources

Semiclassical calculation of nonadiabatic thermal rate constants: application to condensed phase reactions.

The nonadiabatic transition state theory proposed recently by Zhao et al. [J. Chem. Phys. 121, 8854 (2004)] is extended to calculate rate constants of complex systems by using the Monte Carlo and umbrella sampling methods. Surface hopping molecular dynamics technique is incorporated to take into account the dynamic recrossing effect. A nontrivial benchmark model of the nonadiabatic reaction in the condensed phase is used for the numerical test. It is found that our semiclassical results agree well with those produced by the rigorous quantum mechanical method. Comparing with available analytical approaches, we find that the simple statistical theory proposed by Straub and Berne [J. Chem. Phys. 87, 6111 (1987)] is applicable for a wide friction region although their formula is obtained using Landau-Zener [Phys. Z. Sowjetunion 2, 46 (1932); Proc. R. Soc. London, Ser. A 137, 696 (1932)] nonadiabatic transition probability along a one-dimensional diffusive coordinate. We also investigate how the nuclear tunneling events affect the dependence of the rate constant on the friction.

Journal Article↗

Identifying Hfq-binding small RNA targets in Escherichia coli.

The Hfq-binding small RNAs (sRNAs) have recently drawn much attention as regulators of translation in Escherichia coli. We attempt to identify the targets of this class of sRNAs in genome scale and gain further insight into the complexity of translational regulation induced by Hfq-binding sRNAs. Using a new alignment algorithm, most known negatively regulated targets of Hfq-binding sRNAs were identified. The results also show several interesting aspects of the regulatory function of Hfq-binding sRNAs.

Algorithms↗

Faster and more accurate global protein function assignment from protein interaction networks using the MFGO algorithm.

MOTIVATION: Predicting protein function accurately is an important issue in the post-genomic era. To achieve this goal, several approaches have been proposed deduce the function of unclassified proteins through sequence similarity, co-expression profiles, and other information. Among these methods, the global optimization method (GOM) is an interesting and powerful tool that assigns functions to unclassified proteins based on their positions in a physical interactions network [Vazquez, A., Flammini, A., Maritan, A. and Vespignani, A. (2003) Global protein function prediction from protein-protein interaction networks, Nat. Biotechnol., 21, 697-700]. To boost both the accuracy and speed of GOM, a new prediction method, MFGO (modified and faster global optimization) is presented in this paper, which employs local optimal repetition method to reduce calculation time, and takes account of topological structure information to achieve a more accurate prediction. CONCLUSION: On four proteins interaction datasets, including Vazquez dataset, YP dataset, DIP-core dataset, and SPK dataset, MFGO was tested and compared with the popular MR (majority rule) and GOM methods. Experimental results confirm MFGO's improvement on both speed and accuracy. Especially, MFGO method has a distinctive advantage in accurately predicting functions for proteins with few neighbors. Moreover, the robustness of the approach was validated both in a dataset containing a high percentage of unknown proteins and a disturbed dataset through random insertion and deletion. The analysis shows that a moderate amount of misplaced interactions do not preclude a reliable function assignment.

Algorithms↗

Experimental quantum key distribution with decoy states.

To increase dramatically the distance and the secure key generation rate of quantum key distribution (QKD), the idea of quantum decoys--signals of different intensities--has recently been proposed. Here, we present the first experimental implementation of decoy state QKD. By making simple modifications to a commercial quantum key distribution system, we show that a secure key generation rate of 165 bit/s, which is 1/4 of the theoretical limit, can be obtained over 15 km of a telecommunication fiber. We also show that with the same experimental parameters, not even a single bit of secure key can be extracted with a non-decoy-state protocol. Compared to building single photon sources, decoy state QKD is a much simpler method for increasing the distance and key generation rate of unconditionally secure QKD.

Journal Article↗

Involvement of Niemann-Pick type C2 protein in hematopoiesis regulation.

Niemann-Pick type C2 (NPC2) protein has been characterized as a cholesterol-binding protein. Its loss leads to NPC2 disease, an inherited neurodegenerative disorder. When analyzing gene expression profile, we noticed high expression of both NPC2 and its receptor, mannose 6-phosphate receptor (MPR), in murine hematopoietic stem cells. NPC2 protein, in the presence of thrombopoietin (TPO), causes an increase in CFU-GEMM (colony-forming unit-granulocyte-erythroid-macrophage-megakaryocyte) and a decrease in CFU-GM (colony-forming unit-granulocyte-macrophage) colony number in colony-forming cell (CFC) assays. This effect is independent of cholesterol binding but does require the presence of MPR. With M07e cells, a TPO-dependent hematopoietic leukemia cell line, NPC2 can inhibit TPO-induced differentiation and enhance TPO-mediated anti-apoptosis effects. Strikingly, these results are not observed under the standard 20% O(2) level of the standard incubator, but rather at 7% O(2), the physiological oxygen level of bone marrow. Furthermore, NPC2 protein upregulates hypoxia inducible factor 1-alpha protein level at 7% O(2), but not at 20% O(2). Our results demonstrate that NPC2 protein plays a role in hematopoiesis at the physiologic bone marrow level of O(2).

Animals↗

Retinoid-mediated stimulation of steroid sulfatase activity in myeloid leukemic cell lines requires RARalpha and RXR and involves the phosphoinositide 3-kinase and ERK-MAP kinase pathways.

All-trans retinoic acid and 9-cis-retinoic acid stimulate the activity of steroid sulfatase in HL60 acute myeloid leukemia cells in a concentration- and time-dependent manner. Neither of these 'natural retinoids' augmented steroid sulfatase activity in a HL60 sub-line that expresses a dominant-negative retinoic acid receptor alpha (RARalpha). Experiments with synthetic RAR and RXR agonists and antagonists suggest that RARalpha/RXR heterodimers play a role in the retinoid-stimulated increase in steroid sulfatase activity. The retinoid-driven increase in steroid sulfatase activity was attenuated by inhibition of phospholipase D (PLD), but not by inhibitors of phospholipase C. Experiments with inhibitors of protein kinase C (PKC) show that PKCalpha and PKCdelta play an important role in modulating the retinoid-stimulation of steroid sulfatase activity in HL60 cells. Furthermore, we show that pharmacological inhibition of the RAF-1 and ERK MAP kinases blocked the retinoid-stimulated increase in steroid sulfatase activity in HL60 cells and, by contrast, inhibition of the p38-MAP kinase or JNK-MAP kinase had no effect. Pharmacological inhibitors of the phosphatidylinositol 3-kinase, Akt, and PDK-1 also abrogated the retinoid-stimulated increase in steroid sulfatase activity in HL60 cells. These results show that crosstalk between the retinoid-stimulated genomic and non-genomic pathways is necessary to increase steroid sulfatase activity in HL60 cells.

Cells, Cultured↗

NPInter: the noncoding RNAs and protein related biomacromolecules interaction database.

The noncoding RNAs and protein related biomacromolecules interaction database (NPInter; http://bioinfo.ibp.ac.cn/NPInter or http://www.bioinfo.org.cn/NPInter) is a database that documents experimentally determined functional interactions between noncoding RNAs (ncRNAs) and protein related biomacromolecules (PRMs) (proteins, mRNAs or genomic DNAs). NPInter intends to provide the scientific community with a comprehensive and integrated tool for efficient browsing and extraction of information on interactions between ncRNAs and PRMs. Beyond cataloguing details of these interactions, the NPInter will be useful for understanding ncRNA function, as it adds a very important functional element, ncRNAs, to the biomolecule interaction network and sets up a bridge between the coding and the noncoding kingdoms.

Animals↗

HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma.

Tumor-associated antigens (TAAs) have been the most actively employed targets in the clinical diagnosis and treatment of human carcinoma, such as PSA in the diagnosis of prostate cancer and NY-ESO-1 in the immunotherapy of melanoma and other cancers. However, identification of TAAs has often been hampered by the complicated and laborsome laboratory procedures. In order to accelerate the process of tumor antigen discovery, and thereby improve diagnosis and treatment of human carcinoma, we have made an effort to establish a publicly available Human Potential Tumor Associated Antigen database (HPtaa) with potential TAAs identified by in silico computing (http://www.hptaa.org). Tumor specificity was chosen as the core of tumor antigen evaluation, together with other relevant clues. Various platforms of gene expression, including microarray, expressed sequence tag and SAGE data, were processed and integrated by several penalty algorithms. A total of 3518 potential TAAs have been included in the database, which is freely available to academic users. As far as we know, this database is the first one addressing human potential TAAs, and the first one integrating various kinds of expression platforms for one purpose.

Antigens, Neoplasm↗

PINK1 mutations in sporadic early-onset Parkinson's disease.

Pathogenic PINK1 mutations have been described in PARK6-linked Parkinson's disease (PD) patients of Asian origin. However, data on the frequency of PINK1 mutations in sporadic early-onset Parkinson's disease (EOPD) Asian patients are lacking. The objectives of this study were to report the frequency of PINK1 mutations of sporadic EOPD in an Asian cohort comprising of ethnic Chinese, Malays, and Indians, and to highlight a PINK1-positive patient who presented with restless legs symptoms. Eighty consecutive sporadic EOPD patients from the movement disorder clinics of two major tertiary institutions in the country were included. We performed sequence analysis of all the coding and exon-intron junctions of the PINK1 using specific primer sets. In addition, we genotyped polymorphisms detected from the analysis in a group of sporadic PD patients and controls. Three different mutations (two homozygous nonsense and one heterozygous missense) in the putative kinase domain were found in three patients, giving a 3.7% frequency of PINK1 mutations in our EOPD cohort. All the mutations were absent in 200 healthy controls. One patient with a novel homozygous nonsense PINK1 mutation presented unusually with restless legs symptoms. Separately, analysis of the frequency of four PINK1 polymorphisms in a group of sporadic PD and controls did not reveal any significant differences. We highlight a 3.7% frequency of PINK1 mutations in an Asian cohort (ethnic Chinese, Malay, and Indian) of EOPD. The phenotypic spectrum associated with PINK1-positive patients may be wider than previously reported. Polymorphisms of PINK1 do not appear to modulate risk of PD in our population.

Adult↗

Case-control study of UCHL1 S18Y variant in Parkinson's disease.

A recent meta-analysis observed a greater significant inverse association of the ubiquitin carboxy-terminal hydrolase L1 (UCHL1) S18Y variant with Parkinson's disease (PD) for Asian (predominantly Japanese) populations compared with Caucasian populations. We performed an independent case-control study in 335 PD and 341 control subjects with data from a Chinese population to investigate the age-of-onset effect of the UCHL1 variant in PD. The Y/Y and Y/S genotypes were less frequent in the PD young-onset group than in controls and the frequency of the Y alleles was higher in young controls compared to young-onset PD (age at examination <or= 65 years; P = 0.003). Multivariate analysis revealed the Y/Y genotype was significantly lower (P = 0.008) in the young-onset PD (Y/Y vs. S/S: odds ratio [OR]: 0.42; 95% confidence interval [CI]: 0.24, 0.74; S/Y vs. S/S: OR: 0.66, 95% CI: 0.41, 1.08) compared with controls, but this difference was not seen for the late-onset PD. Kaplan-Meier analysis carried out on PD subjects demonstrated that the Y/Y genotype was associated with a later onset of PD than Y/S plus S/S genotypes (P = 0.05). We provided an independent confirmation of the protective effect of the UCHL1 S18Y variant (Y/Y genotype) against PD in young Chinese subjects. Further functional studies of the S18Y variant in both cell and animal models will be of interest.

Adult↗

A case of subcutaneous phaeohyphomycosis caused by Chaetomium globosum and the sequences analysis of C. globosum.

A 14-year-old boy developed painful erythema and necrosis on his face with petechia on his upper extremities. Microscopically, necrotic tissue treated with potassium hydroxide showed branched, dematiaceous, septate hyphae. Chaetomium globosum was isolated repeatedly from the necrotic tissues. Morphology and thermotolerance test of the pathogen were also studied. The internal transcribed spacer region in rRNA gene was amplified and sequenced. The sequence of this patient matched well with that of C. globosum in GenBank and from other patients and environment.

Adolescent↗

Activation of cerebral peroxisome proliferator-activated receptors gamma promotes neuroprotection by attenuation of neuronal cyclooxygenase-2 overexpression after focal cerebral ischemia in rats.

Up-regulation of cyclooxygenase (COX)-2 exacerbates neuronal injury after cerebral ischemia and contributes to neuronal cell death. The present study clarifies the function of cerebral peroxisome-proliferator-activated receptor(s) gamma (PPARgamma) in the expression of COX-2 in neurons of the rat brain after middle cerebral artery occlusion (MCAO) with reperfusion by immunohistochemistry, Western blot, and immunofluorescence staining. In peri-infarct cortical areas the PPARgamma was located in both microglia and neurons, whereas COX-2 was almost exclusively expressed in neurons. PPARgamma immunolabeling reached the peak 12 h after MCAO, whereas the number of COX-2 immunostained cells gradually rose and reached its peak at 48 h. Intracerebroventricular infusion of pioglitazone, an agonist of the PPARgamma, over a 5-day period before and 2 days after MCAO, reduced the infarct size, the expression of tumor necrosis factor alpha (TNF-alpha), COX-2, and the number of cells positively stained for COX-1 and COX-2 in the peri-infarct cortical regions. COX-2 induction was also attenuated in the ipsilateral but not in the contralateral hippocampus. In primary cortical neurons expressing the PPARgamma, pioglitazone suppressed COX-2 expression in response to oxidative stress. This protective effect was reversed after cotreatment with GW 9662, a selective antagonist of the PPARgamma, clearly demonstrating a PPARgamma-dependent mechanism. Our data provide evidence that activation of neuronal PPARgamma considerably contributes to neuroprotection by prevention of COX-2 up-regulation in vitro and in peri-infarct brain areas.

Animals↗

[Serum high-sensitivity C-reaction protein and heart fatty acid binding protein level and cardiac accidents in patients with unstable angina pectoris].

OBJECTIVE: To investigate the relationship between serum high-sensitivity C-reaction protein (hs-CRP) and heart fatty acid binding protein (h-FABP) on cardiac accidents in patients with unstable angina pectoris (UAP). METHOD: Serum levels of hs-CRP, h-FABP, cardiac troponin-I (cTn-I) and creatine kinase MB isoenzyme (CK-MB) were measured and cardiac accidents within 2 weeks after the test were observed in 74 patients (male 45) with stable AP (SAP) and 56 patients (male 29) with UAP. RESULTS: The incidence of cardiac accidents was significantly higher in UAP group (26.8%) than that in SAP group (10.53%, P < 0.001). Serum hs-CRP [(7.64 +/- 2.18) mg/L vs. (1.78 +/- 0.62) mg/L, P < 0.001], h-FABP [(16.46 +/- 5.28) microg/L vs. (3.15 +/- 2.61) microg/L, P < 0.001] and cTn-I [(1.28 +/- 0.43) microg/L vs. (0.67 +/- 0.09) microg/L, P < 0.001] levels were also significantly higher in UAP group than those in SAP group. The serum hs-CRP and h-FABP levels for patients with cardiac accidents in the SAP group were (6.32 +/- 2.06) microg/L and (8.76 +/- 3.83) microg/L respectively, which were higher than those for the patients having no cardiac accidents in the control (P < 0.01). The serum hs-CRP, h-FABP, cTn-I and CK-MB levels in patients with cardiac accidents were significantly higher than those in patients without cardiac accidents in both SAP and UAP groups. CONCLUSION: Measuring traditional parameters for myocardial damage (cTn-I and CK-MB) in combination with hs-CRP and h-FABP is valuable for predicting the risk of recent cardiac accidents for AP patients.

Adult↗

Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression.

Recent evidence points to considerable transcription occurring in non-protein-coding regions of eukaryote genomes. However, their lack of conservation and demonstrated function have created controversy over whether these transcripts are functional. Applying a novel cloning strategy, we have cloned 100 novel and 61 known or predicted Caenorhabditis elegans full-length ncRNAs. Studying the genomic environment and transcriptional characteristics have shown that two-thirds of all ncRNAs, including many intronic snoRNAs, are independently transcribed under the control of ncRNA-specific upstream promoter elements. Furthermore, the transcription levels of at least 60% of the ncRNAs vary with developmental stages. We identified two new classes of ncRNAs, stem-bulge RNAs (sbRNAs) and snRNA-like RNAs (snlRNAs), both featuring distinct internal motifs, secondary structures, upstream elements, and high and developmentally variable expression. Most of the novel ncRNAs are conserved in Caenorhabditis briggsae, but only one homolog was found outside the nematodes. Preliminary estimates indicate that the C. elegans transcriptome contains approximately 2700 small non-coding RNAs, potentially acting as regulatory elements in nematode development.

Animals↗

Gene regulation profile reveals consistent anticancer properties of progesterone in hormone-independent breast cancer cells transfected with progesterone receptor.

Absence of estrogen receptor (ER) and progesterone receptor (PR) is the hallmark of most hormone-independent breast cancers. Previous studies demonstrated that reactivation of PR expression in hormone-independent MDA-MB-231 breast cancer cells enabled progesterone to suppress cell growth both in vitro and in vivo. We determined the whole genomic effect of progesterone in PR-transfected MDA-MB-231 cells. We identified 151 progesterone-regulated genes with expression changes > 3-fold after 24 hr treatment. Most are novel progesterone target genes. Real-time RT-PCR analysis of 55 genes showed a 100% confirmation rate. Twenty-six genes were regulated at both 3 and 24 hr. Studies using translation inhibitor suggest that most of the 26 genes are primary progesterone target genes. Progesterone consistently suppressed the expression of genes required for cell proliferation and metastasis and increased the expression of many tumor-suppressor genes. Progesterone also consistently decreased the expression of DNA repair and chromosome maintenance genes, which may be part of the mechanism leading to cell cycle arrest. These data suggest potential usefulness of progestin in combating ER-negative but PR-positive breast cancer and indicate that progesterone can exert a strong anticancer effect in hormone-independent breast cancer following PR reactivation. The identification of many novel progesterone target genes open up new avenues for in-depth elucidation of progesterone-mediated molecular networks.

Breast Neoplasms↗

An efficient approach for self-consistent-field energy and energy second derivatives in the atomic-orbital basis.

Based on self-consistent-field (SCF) perturbation theory, we recast the SCF and the coupled-perturbed SCF (CPSCF) equations for time-independent molecular properties into the atomic-orbital basis. The density matrix and the perturbed density matrix are obtained iteratively by solving linear equations. Only matrix multiplications and additions are required, and this approach can exploit sparse matrix multiplications and thereby offer the possibility of evaluating second-order properties in computational effort that scales linearly with system size. Convergence properties are similar to conventional molecular-orbital-based CPSCF procedures, in terms of the number of derivative Fock matrices that must be constructed. We also carefully address the issue of the numerical accuracy of the calculated second derivatives of the energy, in order to specify the minimum precision necessary in the CPSCF procedure. It is found that much looser tolerances for the perturbed density matrices are adequate when using an expression for the second derivatives that is correct through second order in the CPSCF error.

Algorithms↗

Genome-wide analysis of mammalian DNA segment fusion/fission.

As a powerful tool for gene function prediction, gene fusion has been widely studied in prokaryotes and certain groups of eukaryotes, but it has been little applied in studies of mammalian genomes. With the first fully sequenced mammalian genomes (human, mouse, rat) now available, we defined and collected a set of fusion/fission event-linked segments (FFLS) based on structured organized genomic alignment. The statistics of the sequence features highlighted the FFLSs against their random context. We found that there are three groups of FFLSs with different component pairs (i.e. gene-gene, gene-noncoding and noncoding-noncoding) in all three mammalian genomes. The proteins encoded by the components of FFLSs in the first group shown a strong tendency to interact with each other. The segmental components in the last two groups which did not contain any protein-coding genes, were found not only to be transcribed to some level, but also more conserved than the random background. Thus, these segments are possibly carrying certain biologically functional elements. We propose that FFLS may be a potential tool for prediction and analysis of function and functional interaction of genetic elements, including both genes and noncoding elements, in mammalian genomes. The full list of the FFLSs in the genomes of the three mammals is available as supporting information at doi:10.1016/j.jtbi.2005.09.016.

Animals↗

Endometriosis-specific genes identified by real-time reverse transcription-polymerase chain reaction expression profiling of endometriosis versus autologous uterine endometrium.

CONTEXT: The etiology and molecular pathogenesis of endometriosis, a prevalent estrogen-dependent gynecologic disease, are poorly understood. OBJECTIVE: The objective of the study was to identify the differentially expressed genes between autologous ectopic and eutopic endometrium. DESIGN: Subtractive hybridization was used for a genome-wide search for differentially expressed genes between autologous ectopic and eutopic endometrium. Real-time RT-PCR was used for gene expression profiling in the paired tissue samples taken from multiple subjects. PATIENTS: The paired pelvic endometriosis and uterine endometrium tissue biopsies were procured from 15 patients undergoing laparoscopy or hysterectomy for endometriosis. RESULTS: Seventy-eight candidate genes were identified from the subtractive cDNA libraries. Seventy-six of these genes were investigated in approximately 8000 real-time PCR for their differential expression in 30 paired tissue biopsies from 15 patients affected by endometriosis. Cluster analysis on gene expression revealed highly consistent profiles in two groups of genes, despite the clinical heterogeneity of the 15 cases. Thirty-four genes specific to early disease point to their potential roles in establishment and evolution of endometriosis. Most interestingly, 14 genes were consistently dysregulated in the paired samples from the majority of the patients. Of these, there were two uncharacterized transcripts and two novel genes, and 10 were matched to known genes: IGFBP5, PIM2, RPL41, PSAP, FBLN1, SIPL, DLX5, HSD11B2, SET, and RHOE. CONCLUSIONS: Dysregulation of 14 genes was found to be overtly associated with endometriosis. Some of these genes, known to participate in estrogen activities and antiapoptosis, may play a role in the pathogenesis of endometriosis and may represent potential diagnostic markers or therapeutic targets for endometriosis.

Adult↗