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101.
Paras Sehgal Samatha Mathew Ambily Sivadas Arjun Ray Jyoti Tanwar Sushma Vishwakarma Gyan Ranjan K V Shamsudheen Rahul C Bhoyar Abhishek Pateria Elvin Leonard Mukesh Lalwani Archana Vats Rajeev R Pappuru Mudit Tyagi Saumya Jakati Shantanu Sengupta Binukumar B K Subhabrata Chakrabarti Inderjeet Kaur Rajender K Motiani Vinod Scaria Sridhar Sivasubbu 《The EMBO journal》2021,40(15)
Long non‐coding RNAs (lncRNAs) are emerging as key regulators of endothelial cell function. Here, we investigated the role of a novel vascular endothelial‐associated lncRNA (VEAL2) in regulating endothelial permeability. Precise editing of veal2 loci in zebrafish (veal2 gib005Δ8/+) induced cranial hemorrhage. In vitro and in vivo studies revealed that veal2 competes with diacylglycerol for interaction with protein kinase C beta‐b (Prkcbb) and regulates its kinase activity. Using PRKCB2 as bait, we identified functional ortholog of veal2 in humans from HUVECs and named it as VEAL2. Overexpression and knockdown of VEAL2 affected tubulogenesis and permeability in HUVECs. VEAL2 was differentially expressed in choroid tissue in eye and blood from patients with diabetic retinopathy, a disease where PRKCB2 is known to be hyperactivated. Further, VEAL2 could rescue the effects of PRKCB2‐mediated turnover of endothelial junctional proteins thus reducing hyperpermeability in hyperglycemic HUVEC model of diabetic retinopathy. Based on evidence from zebrafish and hyperglycemic HUVEC models and diabetic retinopathy patients, we report a hitherto unknown VEAL2 lncRNA‐mediated regulation of PRKCB2, for modulating junctional dynamics and maintenance of endothelial permeability. 相似文献
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103.
In this combined MD simulation and DFT study, interactions of the wild-type (WT) amyloid precursor protein (APP) and its Swedish variant (SW), Lys670 → Asn and Met671 → Leu, with the beta-secretase (BACE1) enzyme and their cleavage mechanisms have been investigated. BACE1 catalyzes the rate-limiting step in the generation of 40-42 amino acid long Alzheimer amyloid beta (Aβ) peptides. All key structural parameters such as position of the flap, volume of the active site, electrostatic binding energy, structures, and positions of the inserts A, D, and F and 10s loop obtained from the MD simulations show that, in comparison to the WT-substrate, BACE1 exhibits greater affinity for the SW-substrate and orients it in a more reactive conformation. The enzyme-substrate models derived from the MD simulations were further utilized to investigate the general acid/base mechanism used by BACE1 to hydrolytically cleave these substrates. This mechanism proceeds through the following two steps: (1) formation of the gem-diol intermediate and (2) cleavage of the peptide bond. For the WT-substrate, the overall barrier of 22.4 kcal/mol for formation of the gem-diol intermediate is 3.3 kcal/mol higher than for the SW-substrate (19.1 kcal/mol). This process is found to be the rate-limiting in the entire mechanism. The computed barrier is in agreement with the measured barrier of ca. 18.00 kcal/mol for the WT-substrate and supports the experimental observation that the cleavage of the SW-substrate is 60 times more efficient than the WT-substrate. 相似文献
104.
Shubhra Singh Rajeev Kumar Srivastava Mukesh Srivastava S.K. Puri K. Srivastava 《Experimental parasitology》2011,(1):318-321
Studies were carried out to establish the potential of RPNI medium for drug-sensitivity studies using the MSF assay. The drug sensitivity of standard anti-malarials was compared using both the (3H) Hypoxanthine incorporation assay and the MSF assay. The media supplements used during the study have been human serum, FBS and ALBUMAX-II. Drug sensitivity of two parasite lines, adapted to grow separately in conventional as well as in RPNI medium was compared to observe the effect of RPNI medium on functional characteristics of the parasite. The results revealed identical IC50 values of standard anti-malarials obtained by both the (3H) Hypoxanthine incorporation assay and the MSF assay and no untoward effect of FBS and ALBUMAX-II could be noticed on the chemo-sensitivity of standard anti-malarials. Apart from this the chemo-sensitive response of parasite line adapted to grow in RPNI medium was observed to be intact. These findings showed that RPNI medium has potential to be used for chemo-sensitivity studies and the MSF assay being more convenient was observed to be most suitable assay for bio evaluation of new molecules. 相似文献
105.
Because the properties of horizontally-transferred genes will reflect the mutational proclivities of their donor genomes, they often show atypical compositional properties relative to native genes. Parametric methods use these discrepancies to identify bacterial genes recently acquired by horizontal transfer. However, compositional patterns of native genes vary stochastically, leaving no clear boundary between typical and atypical genes. As a result, while strongly atypical genes are readily identified as alien, genes of ambiguous character are poorly classified when a single threshold separates typical and atypical genes. This limitation affects all parametric methods that examine genes independently, and escaping it requires the use of additional genomic information. We propose that the performance of all parametric methods can be improved by using a multiple-threshold approach. First, strongly atypical alien genes and strongly typical native genes would be identified using conservative thresholds. Genes with ambiguous compositional features would then be classified by examining gene context, including the class (native or alien) of flanking genes. By including additional genomic information in a multiple-threshold framework, we observed a remarkable improvement in the performance of several popular, but algorithmically distinct, methods for alien gene detection. 相似文献
106.
Athar M Chaudhury NK Hussain ME Varshney R 《Molecular and cellular biochemistry》2011,352(1-2):281-292
Oxidative stress and mitochondrial dysfunction in cancer cells represent features that may be exploited therapeutically. We determined whether minor groove binding ligand Hoechst 33342, known to induce mitochondrial dysfunction via increase in reactive oxygen species (ROS), enhances killing of human head and neck cancer (KB) cells mediated by impaired expression of mitochondrial protein involved in electron transfer. Elevation in ROS generation, increase in ΔΨm, down regulation of cytochrome c oxidase (CO), alteration in expression of antioxidant enzymes viz. Mn-SOD and Catalase, and release of cytochrome c into the cytosol, were observed in time-dependent manner when cells were irradiated (5 Gy) in presence of Hoechst 33342. Persistent increase in ROS observed till 48 h following treatment decreased the clonogenic survival and viability to a large extent via increase in ΔΨm, release of cytochrome c and non-coordinated expression of antioxidant enzymes. Treatment with antioxidants PEG-MnSOD and PEG-catalase inhibited the increase in ROS and loss of cell survival, suggesting the involvement of ROS in the Hoechst 33342-induced cell death. The result demonstrated significant sensitization of cancer cells to radiation-induced toxicity in presence of Hoechst 33342 via increasing ROS to a toxic level and impairing CO expression and antioxidant enzymes. This understanding is expected to benefit both in elucidating the detailed mechanisms of actions of DNA interacting drug and designing better molecules for enhancing radiation-induced cell death among cancer cells. 相似文献
107.
108.
109.
Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis 总被引:1,自引:0,他引:1
Linhai Wang Sheng Yu Chaobo Tong Yingzhong Zhao Yan Liu Chi Song Yanxin Zhang Xudong Zhang Ying Wang Wei Hua Donghua Li Dan Li Fang Li Jingyin Yu Chunyan Xu Xuelian Han Shunmou Huang Shuaishuai Tai Junyi Wang Xun Xu Yingrui Li Shengyi Liu Rajeev K Varshney Jun Wang Xiurong Zhang 《Genome biology》2014,15(2):R39
110.
Entropy based measures have been frequently used in symbolic sequence analysis. A symmetrized and smoothed form of Kullback-Leibler divergence or relative entropy, the Jensen-Shannon divergence (JSD), is of particular interest because of its sharing properties with families of other divergence measures and its interpretability in different domains including statistical physics, information theory and mathematical statistics. The uniqueness and versatility of this measure arise because of a number of attributes including generalization to any number of probability distributions and association of weights to the distributions. Furthermore, its entropic formulation allows its generalization in different statistical frameworks, such as, non-extensive Tsallis statistics and higher order Markovian statistics. We revisit these generalizations and propose a new generalization of JSD in the integrated Tsallis and Markovian statistical framework. We show that this generalization can be interpreted in terms of mutual information. We also investigate the performance of different JSD generalizations in deconstructing chimeric DNA sequences assembled from bacterial genomes including that of E. coli, S. enterica typhi, Y. pestis and H. influenzae. Our results show that the JSD generalizations bring in more pronounced improvements when the sequences being compared are from phylogenetically proximal organisms, which are often difficult to distinguish because of their compositional similarity. While small but noticeable improvements were observed with the Tsallis statistical JSD generalization, relatively large improvements were observed with the Markovian generalization. In contrast, the proposed Tsallis-Markovian generalization yielded more pronounced improvements relative to the Tsallis and Markovian generalizations, specifically when the sequences being compared arose from phylogenetically proximal organisms. 相似文献