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Background
The DNase I hypersensitive sites (DHSs) are associated with the cis-regulatory DNA elements. An efficient method of identifying DHSs can enhance the understanding on the accessibility of chromatin. Despite a multitude of resources available on line including experimental datasets and computational tools, the complex language of DHSs remains incompletely understood.Methods
Here, we address this challenge using an approach based on a state-of-the-art machine learning method. We present a novel convolutional neural network (CNN) which combined Inception like networks with a gating mechanism for the response of multiple patterns and longterm association in DNA sequences to predict multi-scale DHSs in Arabidopsis, rice and Homo sapiens.Results
Our method obtains 0.961 area under curve (AUC) on Arabidopsis, 0.969 AUC on rice and 0.918 AUC on Homo sapiens.Conclusions
Our method provides an efficient and accurate way to identify multi-scale DHSs sequences by deep learning.83.
In vitro and clinical data analysis of Osteopontin as a prognostic indicator in colorectal cancer 下载免费PDF全文
Ran Wei Janet Pik Ching Wong Peng Lyu Xinping Xi Olivia Tong Shu‐Dong Zhang Hiu Fung Yuen Senji Shirasawa Hang Fai Kwok 《Journal of cellular and molecular medicine》2018,22(9):4097-4105
Osteopontin (OPN) has been shown to promote colorectal cancer (CRC) progression; however, the mechanism of OPN‐induced CRC progression is largely unknown. In this study, we found that OPN overexpression led to enhanced anchorage‐independent growth, cell migration and invasion in KRAS gene mutant cells but to a lesser extent in KRAS wild‐type cells. OPN overexpression also induced PI3K signalling, expression of Snail and Matrix metallopeptidase 9 (MMP9), and suppressed the expression of E‐cadherin in KRAS mutant cells. In human CRC specimens, a high‐level expression of OPN significantly predicted poorer survival in CRC patients and OPN expression was positively correlated with MMP9 expression, and negatively correlated with E‐cadherin expression. Furthermore, we have found that 15 genes were co‐upregulated in OPN highly expression CRC and a list of candidate drugs that may have potential to reverse the secreted phosphoprotein 1 (SPP1) gene signature by connectivity mapping. In summary, OPN is a potential prognostic indicator and therapeutic target for colon cancer. 相似文献
84.
Soil temperature is known to affect plant growth and productivity. In this study we found that low root-zone temperature (LRT) inhibited the growth of apple (Malus baccata Borkh.) seedlings. To elucidate the molecular mechanism of LRT response, we performed comparative proteome analysis of the apple roots under LRT for 6 days. Total proteins of roots were extracted and separated by two-dimensional gel electrophoresis (2-DE) and 29 differentially accumulated proteins were successfully identified by MALDI-TOF/TOF mass spectrometry. They were involved in protein transport/processing/degradation (21%), glycometabolism (20%), response to stress (14%), oxidoreductase activity (14%), protein binding (7%), RNA metabolism (7%), amino acid biosynthesis (3%) and others (14%). The results revealed that LRT inhibited glycometabolism and RNA metabolism. The up-regulated proteins which were associated with oxidoreductase activity, protein metabolism and defense response, might be involved in protection mechanisms against LRT stress in the apple seedlings. Subsequently, 8 proteins were selected for the mRNA quantification analysis, and we found 6 of them were consistently regulated between protein and mRNA levels. In addition, the enzyme activities in ascorbate–glutathione (AsA–GSH) cycle were determined, and APX activity was increased and GR activity was decreased under LRT, in consistent with the protein levels. This study provides new insights into the molecular mechanisms of M. baccata in responding to LRT. 相似文献
85.
Effects of exogenous phenolic acids on photosystem functions and photosynthetic electron transport rate in strawberry leaves 总被引:2,自引:0,他引:2
X. F. Lu H. Zhang S. S. Lyu G. D. Du X. Q. Wang C. H. Wu D. G. Lyu 《Photosynthetica》2018,56(2):616-622
Our study investigated the physiological and biochemical basis for the effects of exogenous phenolic acids on the function of the photosynthetic apparatus and photosynthetic electron transport rate in strawberry seedlings. Potted seedlings of the strawberry (Fragaria × ananassa Duch.) were used. Syringic acid inhibited net photosynthetic rate and water-use efficiency decreased. Additionally, primary quinone electron acceptor of the PSII reaction centre, the PSII reaction centre and the oxygen evolving complex were also impaired. Both the maximum quantum yield of the PSII primary photochemistry and the performance index on absorption basis were depressed, resulting in reduced function of the photosynthetic electron transport chain. Otherwise, low phthalic acid concentrations enhanced photosynthetic capacity, while high concentrations showed opposite effects. Syringic acid exhibited a higher toxic effect than that of phthalic acid which was more evident at higher concentrations. 相似文献
86.
Activated proline‐rich tyrosine kinase 2 regulates meiotic spindle assembly in the mouse oocyte 下载免费PDF全文
Xiao‐Qian Meng Bing Cui Dong Cheng Hui Lyu Li‐Gang Jiang Ke‐Gang Zheng Shu‐Zhen Liu Jie Pan Cong Zhang Jing Bai Jun Zhou 《Journal of cellular biochemistry》2018,119(1):736-747
Proline‐rich tyrosine kinase 2 (PYK2), a member of the protein tyrosine kinase family, plays an important role in various cellular processes. PYK2 can be phosphorylated on tyrosine 402 by diverse stimuli at the cell surface, and recent studies have shown that this activated form of PYK2 is enriched in oocytes and required for fertilization. However, the subcellular localization and functions of activated PYK2 in oocytes remain elusive. In this study, we demonstrate that the localization of p‐PYK2 undergoes dynamic changes during in vitro maturation of mouse oocytes. The signal of p‐PYK2 is initially dispersed in the cytoplasm, but begins to decorate organized microtubules after the germinal vesicle breakdown and localizes to spindle poles at metaphase. Our data further show that p‐PYK2 colocalizes with γ‐tubulin from the germinal vesicle stage through the end of meiosis in mouse oocytes. Nocodazole treatment and washout experiments confirm that p‐PYK2 associates with the oocyte spindle and spindle poles. Moreover, pharmacological inhibition of PYK2 activity dramatically alters the morphology of the bipolar spindle and prevents oocyte maturation. Together, these data suggest that activated PYK2 may function as a component of the microtubule organizing center to regulate spindle assembly during the meiotic process of mouse oocytes. 相似文献
87.
Several models for the origin of life involve molecules that are capable of self-replication, such as self-replicating polymers composed of RNA or DNA or amino acids. Here we consider a hypothetical replicator (AB) composed of two subunits, A and B. Programs written in Python and C programming languages were used to model AB replicator abundance as a function of cycles of replication (iterations), under specified hypothetical conditions. Two non-exclusive models describe how a reduced stability for B relative to A can have an advantage for replicator activity and/or evolution by generating free A subunits. In model 1, free A subunits associate with AB replicators to create AAB replicators with greater activity. In simulations, reduced stability of B was beneficial when the replication activity of AAB was greater than two times the replication activity of AB. In model 2, the free A subunit is inactive for some number of iterations before it re-creates the B subunit. A re-creates the B subunit with an equal chance of creating B or B′, where B′ is a mutant that increases AB’ replicator activity relative to AB. In simulations, at moderate number of iterations (< 15), a shorter survival time for B is beneficial when the stability of B is greater than the inactive time of A. The results are consistent with the hypothesis that reduced stability for a replicator subunit can be advantageous under appropriate conditions. 相似文献
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90.
Global patterns of Rhododendron diversity: The role of evolutionary time and diversification rates 下载免费PDF全文
Nawal Shrestha Zhiheng Wang Xiangyan Su Xiaoting Xu Lisha Lyu Yunpeng Liu Dimitar Dimitrov Jonathan D. Kennedy Qinggang Wang Zhiyao Tang Xiaojuan Feng 《Global Ecology and Biogeography》2018,27(8):913-924