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141.
Population viability analysis (PVA) entails calculation of extinction risk, as defined by various extinction metrics, for a study population. These calculations strongly depend on the form of the population growth model and inclusion of demographic and/or environmental stochasticity. Form of the model and its parameters are determined based on observed population time series data. A typical population time series, consisting of estimated population sizes, inevitably has some observation error and likely has missing observations. In this paper, we present a likelihood based PVA in the presence of observation error and missing data. We illustrate the importance of incorporation of observation error in PVA by reanalyzing the population time series of song sparrow Melospiza melodia on Mandarte Island, British Columbia, Canada from 1975–1998. Using Akaike information criterion we show that model with observation error fits the data better than the one without observation error. The extinction risks predicted by with and without observation error models are quite different. Further analysis of possible causes for observation error revealed that some component of the observation error might be due to unreported dispersal. A complete analysis of such data, thus, would require explicit spatial models and data on dispersal along with observation error. Our conclusions are, therefore, two‐fold: 1) observation errors in PVA matter and 2) integrating these errors in PVA is not always enough and can still lead to important biases in parameter estimates if other processes such as dispersal are ignored. 相似文献
142.
Yongqian Zhao Tingjin Sherryl Soh Kitti Wing Ki Chan Sarah Suet Yin Fung Kunchithapadam Swaminathan Siew Pheng Lim Pei-Yong Shi Thomas Huber Julien Lescar Dahai Luo Subhash G. Vasudevan 《Journal of virology》2015,89(20):10717-10721
We examined the function of the conserved Val/Ile residue within the dengue virus NS5 interdomain linker (residues 263 to 272) by site-directed mutagenesis. Gly substitution or Gly/Pro insertion after the conserved residue increased the linker flexibility and created slightly attenuated viruses. In contrast, Pro substitution abolished virus replication by imposing rigidity in the linker and restricting NS5''s conformational plasticity. Our biochemical and reverse genetics experiments demonstrate that NS5 utilizes conformational regulation to achieve optimum viral replication. 相似文献
143.
144.
Indira Umareddy Olivier Pluquet Qing Yin Wang Subhash G Vasudevan Eric Chevet Feng Gu 《Virology journal》2007,4(1):1-10
Background
Tomato-infecting begomoviruses are widely distributed across the world and cause diseases of high economic impact on wide range of agriculturally important crops. Though recombination plays a pivotal role in diversification and evolution of these viruses, it is currently unknown whether there are differences in the number and quality of recombination events amongst different tomato-infecting begomovirus species. To examine this we sought to characterize the recombination events, estimate the frequency of recombination, and map recombination hotspots in tomato-infecting begomoviruses of South and Southeast Asia.Results
Different methods used for recombination breakpoint analysis provided strong evidence for presence of recombination events in majority of the sequences analyzed. However, there was a clear evidence for absence or low Recombination events in viruses reported from North India. In addition, we provide evidence for non-random distribution of recombination events with the highest frequency of recombination being mapped in the portion of the N-terminal portion of Rep.Conclusion
The variable recombination observed in these viruses signified that all begomoviruses are not equally prone to recombination. Distribution of recombination hotspots was found to be reliant on the relatedness of the genomic region involved in the exchange. Overall the frequency of phylogenetic violations and number of recombination events decreased with increasing parental sequence diversity. These findings provide valuable new information for understanding the diversity and evolution of tomato-infecting begomoviruses in Asia. 相似文献145.
Bhushan S Kumar A Malik F Andotra SS Sethi VK Kaur IP Taneja SC Qazi GN Singh J 《Apoptosis : an international journal on programmed cell death》2007,12(10):1911-1926
A triterpenediol (TPD) comprising of isomeric mixture of 3α, 24-dihydroxyurs-12-ene and 3α, 24-dihydroxyolean-12-ene from
Boswellia serrata induces apoptosis in cancer cells. An attempt was made in this study to investigate the mechanism of cell death by TPD in
human leukemia HL-60 cells. It inhibited cell proliferation with IC50 ∼ 12 μg/ml and produced apoptosis as measured by various biological end points e.g. increased sub-G0 DNA fraction, DNA ladder
formation, enhanced AnnexinV-FITC binding of the cells. Further, initial events involved massive reactive oxygen species (ROS)
and nitric oxide (NO) formation, which were significantly inhibited by their respective inhibitors. Persistent high levels
of NO and ROS caused Bcl-2 cleavage and translocation of Bax to mitochondria, which lead to loss of mitochondrial membrane
potential (Δψm) and release of cytochrome c, AIF, Smac/DIABLO to the cytosol. These events were associated with decreased expression of
survivin and ICAD with attendant activation of caspases leading to PARP cleavage. Furthermore, TPD up regulated the expression
of cell death receptors DR4 and TNF-R1 level, leading to caspase-8 activation. These studies thus demonstrate that TPD produces
oxidative stress in cancer cells that triggers self-demise by ROS and NO regulated activation of both the intrinsic and extrinsic
signaling cascades. 相似文献
146.
Data cloning: easy maximum likelihood estimation for complex ecological models using Bayesian Markov chain Monte Carlo methods 总被引:1,自引:0,他引:1
We introduce a new statistical computing method, called data cloning, to calculate maximum likelihood estimates and their standard errors for complex ecological models. Although the method uses the Bayesian framework and exploits the computational simplicity of the Markov chain Monte Carlo (MCMC) algorithms, it provides valid frequentist inferences such as the maximum likelihood estimates and their standard errors. The inferences are completely invariant to the choice of the prior distributions and therefore avoid the inherent subjectivity of the Bayesian approach. The data cloning method is easily implemented using standard MCMC software. Data cloning is particularly useful for analysing ecological situations in which hierarchical statistical models, such as state-space models and mixed effects models, are appropriate. We illustrate the method by fitting two nonlinear population dynamics models to data in the presence of process and observation noise. 相似文献
147.
In vitro culture may be the major contributing factor for transgenic versus nontransgenic proteomic plant differences 下载免费PDF全文
Cátia Fonseca Sébastien Planchon Tânia Serra Subhash Chander Nelson J. M. Saibo Jenny Renaut M. Margarida Oliveira Rita Batista 《Proteomics》2015,15(1):124-134
Identification of differences between genetically modified plants and their original counterparts plays a central role in risk assessment strategy. Our main goal was to better understand the relevance of transgene presence, genetic, and epigenetic changes induced by transgene insertion, and in vitro culture in putative unintended differences between a transgenic and its comparator. Thus, we have used multiplex fluorescence 2DE coupled with MS to characterize the proteome of three different rice lines (Oryza sativa L. ssp. japonica cv. Nipponbare): a control conventional line (C), an Agrobacterium‐transformed transgenic line (Ta) and a negative segregant (NSb). We observed that Ta and NSb appeared identical (with only one spot differentially abundant—fold difference ≥ 1.5), contrasting with the control (49 spots with fold difference ≥1.5, in both Ta and NSb vs. control). Given that in vitro culture was the only event in common between Ta and NSb, we hypothesize that in vitro culture stress was the most relevant condition contributing for the observed proteomic differences. MS protein identification support our hypothesis, indicating that Ta and NSb lines adjusted their metabolic pathways and altered the abundance of several stress related proteins in order to cope with in vitro culture. 相似文献
148.
Annedi SC Ramnauth J Cossette M Maddaford SP Dove P Rakhit S Andrews JS Porreca F 《Bioorganic & medicinal chemistry letters》2012,22(7):2510-2513
A novel class of 1,7-disubstituted 2,3,4,5-tetrahydro-1H-benzo[b]azepine derivatives was designed, synthesized and evaluated as human nitric oxide synthase (NOS) inhibitors. Structure-activity relationship studies based on various basic amine side chains attached at the 1-position of the 2,3,4,5-tetrahydro-1H-benzo[b]azepine ring led to the identification of several potent and highly selective inhibitors (17, 18, 25, (±)-39, and (±)-40) of human neuronal NOS. The potential therapeutic application of one of these new selective nNOS inhibitors (17) was demonstrated in an in vivo spinal nerve ligation model of neuropathic pain, and various in vitro safety pharmacology studies such as the hERG K(+) channel inhibition assay and high throughput broad screen (minimal activity at 79 receptors/transporters/ion channels). 相似文献
149.
Verbanac D Jain SC Jain N Chand M Cipčić Paljetak H Matijašić M Perić M Stepanić V Saso L 《Bioorganic & medicinal chemistry》2012,20(10):3180-3185
Xanthones and their thio-derivatives are a class of pleiotropic compounds with various reported pharmacological and biological activities. Although these activities are mainly determined in laboratory conditions, the class itself has a great potential to be utilized as promising chemical scaffold for the synthesis of new drug candidates. One of the main obstacles in utilization of these compounds was related to the difficulties in their chemical synthesis. Most of the known methods require two steps, and are limited to specific reagents not applicable to a large number of starting materials. In this paper a new and improved method for chemical synthesis of xanthones is presented. By applying a new procedure, we have successfully obtained these compounds with the desired regioselectivity in a shorter reaction time (50s) and with better yield (>80%). Finally, the preliminary in vitro screenings on different bacterial species and cytotoxicity assessment, as well as in silico activity evaluation were performed. The obtained results confirm potential pharmacological use of this class of molecules. 相似文献
150.
Kuldeep K. Roy Santoshkumar Tota Tusha Tripathi Subhash Chander Chandishwar Nath Anil K. Saxena 《Bioorganic & medicinal chemistry》2012,20(21):6313-6320
The optimization of our previous lead compound 1 (AChE IC50 = 3.31 μM) through synthesis and pharmacology of a series of novel carbamates is reported. The synthesized compounds were evaluated against mouse brain AChE enzyme using the colorimetric method described by Ellman et al. The three compounds 6a (IC50 = 2.57 μM), 6b (IC50 = 0.70 μM) and 6i (IC50 = 2.56 μM) exhibited potent in vitro AChE inhibitory activities comparable to the drug rivastigmine (IC50 = 1.11 μM). Among them, the compound 6b has been selected as possible optimized lead for further neuropharmacological studies. In addition, the AChE–carbamate Michaelis complexes of these potent compounds including rivastigmine and ganstigmine have been modeled using covalent docking protocol of GOLD and important direct/indirect interactions contributing to stabilization of the AChE–carbamate Michaelis complexes have been investigated. 相似文献