Fangting Li

The yeast cell-cycle network is robustly designed

The interactions between proteins, DNA, and RNA in living cells constitute molecular networks that govern various cellular functions. To investigate the global dynamical properties and stabilities of such networks, we studied the cell-cycle regulatory network of the budding yeast. With the use of a simple dynamical model, it was demonstrated that the cell-cycle network is extremely stable and robust for its function. The biological stationary state, the G1 state, is a global attractor of the dynamics. The biological pathway, the cell-cycle sequence of protein states, is a globally attracting trajectory of the dynamics. These properties are largely preserved with respect to small perturbations to the network. These results suggest that cellular regulatory networks are robustly designed for their functions.

Stochastic model of yeast cell-cycle network

Biological functions in living cells are controlled by protein interaction and genetic networks. These molecular networks should be dynamically stable against various fluctuations which are inevitable in the living world. In this paper, we propose and study a stochastic model for the network regulating the cell cycle of the budding yeast. The stochasticity in the model is controlled by a temperature-like parameter . Our simulation results show that both the biological stationary state and the biological pathway are stable for a wide range of “temperature”. There is, however, a sharp transition-like behavior at c, below which the dynamics are dominated by noise. We also define a pseudo energy landscape for the system in which the biological pathway can be seen as a deep valley. c 2006 Elsevier B.V. All rights reserved.

Constructing the energy landscape for genetic switching system driven by intrinsic noise.

Genetic switching driven by noise is a fundamental cellular process in genetic regulatory networks. Quantitatively characterizing this switching and its fluctuation properties is a key problem in computational biology. With an autoregulatory dimer model as a specific example, we design a general methodology to quantitatively understand the metastability of gene regulatory system perturbed by intrinsic noise. Based on the large deviation theory, we develop new analytical techniques to describe and calculate the optimal transition paths between the on and off states. We also construct the global quasi-potential energy landscape for the dimer model. From the obtained quasi-potential, we can extract quantitative results such as the stationary distributions of mRNA, protein and dimer, the noise strength of the expression state, and the mean switching time starting from either stable state. In the final stage, we apply this procedure to a transcriptional cascades model. Our results suggest that the quasi-potential energy landscape and the proposed methodology are general to understand the metastability in other biological systems with intrinsic noise.

Interleukin-1β Level Is Increased in Vitreous of Patients with Neovascular Age-Related Macular Degeneration (nAMD) and Polypoidal Choroidal Vasculopathy (PCV).

Purpose To examine the expression of pro-interleukin-1β (pro-IL-1β) and interleukin-1β (IL-1β) in the vitreous body of patients with neovascular age-related macular degeneration(nAMD), polypoidal choroidal vasculopathy (PCV), proliferative diabetic retinopathy (PDR), retinal vein occlusion (RVO) or Eales’ disease to further elucidate the role of IL-1β and inflammation in the pathogenesis of neovascular retinal disease. Design Prospective clinical laboratory investigation study. Methods All patients enrolled had vitreous hemorrhage due to nAMD, PCV, PDR, RVO or Eales’ disease that required vitrectomy. Patients were excluded for any history of active intraocular inflammation, or other ophthalmic surgery besides vitrectomy. Control samples were obtained from patients with idiopathic macular epiretinal membrane. A total of fifty vitreous samples were collected from patient during vitrectomy. Pro-IL-1β and IL-1β expression were measured by enzyme-linked immunosorbent assay (ELISA). Results were analyzed statistically using nonparametric tests. Results Expression of pro-IL-1β protein was increased by 2.83-fold and 9.19-fold in PCV and nAMD vitreous samples relative to control, respectively. Expression of IL-β protein was increased by 10-fold and 4.83-fold in PCV and nAMD vitreous samples relative to control, respectively. Conclusions Our results demonstrate that expression of pro-IL-1β and IL-1β proteins is higher in PCV and nAMD. The roles of pro-IL-1β and IL-1β as inflammatory mediators in the development of PCV and nAMD may be associated with photoreceptor degeneration and neovascularization which necessitates further study.

Quercetin Inhibits Vascular Endothelial Growth Factor-Induced Choroidal and Retinal Angiogenesis in vitro

Purpose: The aim of this study was to investigate the effects of quercetin on vascular endothelial growth factor (VEGF)-induced choroidal and retinal angiogenesis in vitro using a rhesus macaque choroid-retinal endothelial (RF/6A) cell line. Methods: RF/6A cells were cultured in Dulbeccos modified Eagles medium containing 10% fetal bovine serum. Then the cells were treated with different concentrations (from 0 to 100 μM) of quercetin and 100 ng/ml VEGF. The cell proliferation was assessed using cholecystokinin octapeptide dye. The cell migration was investigated by a Transwell assay. The tube formation was measured on Matrigel. Furthermore, the impact of quercetins effects on VEGF-induced activation of VEGF receptor 2 (VEGFR-2) downstream signal pathways was tested by Western blot analysis. Results: Quercetin inhibits RF/6A cell proliferation in a dose-dependent fashion: 22.7, 31.5 and 36.7% inhibition on treatment with 10, 50 and 100 μM quercetin, respectively. VEGF-induced migration and tube formation of RF/6A cells were also significantly inhibited by quercetin in a dose-dependent manner. Quercetin inhibits VEGF-induced VEGFR-2 downstream signal pathways of RF/6A. Conclusions: The results show that quercetin inhibits VEGF-induced cell proliferation, migration and tube formation of RF/6A. We suggest that quercetin inhibits VEGF-induced choroidal and retinal angiogenesis in vitro. Collectively, the findings in the present study suggest that quercetin inhibits VEGF-induced choroidal and retinal angiogenesis by targeting the VEGFR-2 pathway. This suggests that quercetin is a choroidal and retinal angiogenesis inhibitor.

Energy landscape reveals that the budding yeast cell cycle is a robust and adaptive multi-stage process.

Quantitatively understanding the robustness, adaptivity and efficiency of cell cycle dynamics under the influence of noise is a fundamental but difficult question to answer for most eukaryotic organisms. Using a simplified budding yeast cell cycle model perturbed by intrinsic noise, we systematically explore these issues from an energy landscape point of view by constructing an energy landscape for the considered system based on large deviation theory. Analysis shows that the cell cycle trajectory is sharply confined by the ambient energy barrier, and the landscape along this trajectory exhibits a generally flat shape. We explain the evolution of the system on this flat path by incorporating its non-gradient nature. Furthermore, we illustrate how this global landscape changes in response to external signals, observing a nice transformation of the landscapes as the excitable system approaches a limit cycle system when nutrients are sufficient, as well as the formation of additional energy wells when the DNA replication checkpoint is activated. By taking into account the finite volume effect, we find additional pits along the flat cycle path in the landscape associated with the checkpoint mechanism of the cell cycle. The difference between the landscapes induced by intrinsic and extrinsic noise is also discussed. In our opinion, this meticulous structure of the energy landscape for our simplified model is of general interest to other cell cycle dynamics, and the proposed methods can be applied to study similar biological systems.

Modular analysis of the probabilistic genetic interaction network

Motivation: Epistatic Miniarray Profiles (EMAP) has enabled the mapping of large-scale genetic interaction networks; however, the quantitative information gained from EMAP cannot be fully exploited since the data are usually interpreted as a discrete network based on an arbitrary hard threshold. To address such limitations, we adopted a mixture modeling procedure to construct a probabilistic genetic interaction network and then implemented a Bayesian approach to identify densely interacting modules in the probabilistic network. Results: Mixture modeling has been demonstrated as an effective soft-threshold technique of EMAP measures. The Bayesian approach was applied to an EMAP dataset studying the early secretory pathway in Saccharomyces cerevisiae. Twenty-seven modules were identified, and 14 of those were enriched by gold standard functional gene sets. We also conducted a detailed comparison with state-of-the-art algorithms, hierarchical cluster and Markov clustering. The experimental results show that the Bayesian approach outperforms others in efficiently recovering biologically significant modules. Contact: dengmh@pku.edu.cn; fangtingli@pku.edu.cn; zhuyp@hupo.org.cn Supplementary Information: Supplementary data are available at Bioinformatics online.

Integrating multiple types of data to predict novel cell cycle-related genes

BackgroundCellular functions depend on genetic, physical and other types of interactions. As such, derived interaction networks can be utilized to discover novel genes involved in specific biological processes. Epistatic Miniarray Profile, or E-MAP, which is an experimental platform that measures genetic interactions on a genome-wide scale, has successfully recovered known pathways and revealed novel protein complexes in Saccharomyces cerevisiae (budding yeast).ResultsBy combining E-MAP data with co-expression data, we first predicted a potential cell cycle related gene set. Using Gene Ontology (GO) function annotation as a benchmark, we demonstrated that the prediction by combining microarray and E-MAP data is generally >50% more accurate in identifying co-functional gene pairs than the prediction using either data source alone. We also used transcription factor (TF)–DNA binding data (Chip-chip) and protein phosphorylation data to construct a local cell cycle regulation network based on potential cell cycle related gene set we predicted. Finally, based on the E-MAP screening with 48 cell cycle genes crossing 1536 library strains, we predicted four unknown genes (YPL158C, YPR174C, YJR054W, and YPR045C) as potential cell cycle genes, and analyzed them in detail.ConclusionBy integrating E-MAP and DNA microarray data, potential cell cycle-related genes were detected in budding yeast. This integrative method significantly improves the reliability of identifying co-functional gene pairs. In addition, the reconstructed network sheds light on both the function of known and predicted genes in the cell cycle process. Finally, our strategy can be applied to other biological processes and species, given the availability of relevant data.

ANALYSIS OF CHANGES IN CHARACTERISTICS OF SEVERE RETINOPATHY OF PREMATURITY PATIENTS AFTER SCREENING GUIDELINES WERE ISSUED IN CHINA.

Purpose: To describe the changes in the characteristics of infants treated for severe retinopathy of prematurity (ROP) in a tertiary referral unit in China after screening guidelines were issued in 2004 and to evaluate the effectiveness of the current criteria. Methods: Information on consecutive infants referred to a single eye department for treatment of Stage 3 (Type 1 pretheshold and threshold disease), Stage 4, and Stage 5 ROP between January 2001 and May 2012 was retrieved from medical records. Results: The mean gestational age was 29.98 ± 2.13 weeks (range 26–34 weeks), and the mean birth weight was 1,414.32 ± 343.18 g (range 742–2,087 g). The proportion of infants with Stage 4 and Stage 5 ROP decreased statistically significantly over time (P = 0.026 and P < 0.001, respectively) after screening guidelines for ROP were issued in 2004. The median postmenstrual age when patients first visited the study hospital was 48.32 weeks (range 30–602 weeks); later presentation was significantly associated with more advanced ROP (P < 0.001). In addition, the postmenstrual age of first presentation showed a significant decrease over time (P < 0.001) after the screening guidelines were issued. The current Chinese screening guidelines cover 99.63% of infants while 9.07% of infants exceeded the U.K. screening criteria and 35.77% of infants exceeded the U.S. criteria. Conclusion: After the government issued guidelines on ROP screening, the birth weight and gestational age of severe ROP patients remain similar. Big infants got severe ROP as before. But the awareness of ROP increased, the proportion of infants with retinal detachment caused by ROP decreased, and the infants received more timely treatment. The current ROP screening criteria are very effective.

ABCA1 rs1883025 Polymorphism Shows No Association with Neovascular Age-Related Macular Degeneration or Polypoidal Choroidal Vasculopathy in a Northern Chinese Population

Purpose: To analyze the association between ABCA1 rs1883025 variants with neovascular age-related macular degeneration (nAMD) and polypoidal choroidal vasculopathy (PCV) in a northern Chinese population. Methods: The study enrolled 900 subjects, including 300 controls, 300 cases with nAMD and 300 cases with PCV. Genomic DNA was extracted from venous blood leukocytes. Single-nucleotide polymorphisms in the ABCA1 (rs1883025) gene were genotyped by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Results: The ABCA1 rs1883025 polymorphism was not significantly associated with nAMD (22.5%; p > 0.05) or PCV (20.8%; p > 0.05) in a northern Chinese population. The association remained insignificant after adjustment for age and gender differences (p > 0.05). Conclusions: This study suggests that ABCA1 rs1883025 variants are not associated with nAMD or PCV in a Chinese population, which is likely due to an ethnic difference.