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61.
Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies 总被引:13,自引:8,他引:5
Estimation of evolutionary distances from coding sequences must take into
account protein-level selection to avoid relative underestimation of longer
evolutionary distances. Current modeling of selection via site-to-site rate
heterogeneity generally neglects another aspect of selection, namely
position-specific amino acid frequencies. These frequencies determine the
maximum dissimilarity expected for highly diverged but functionally and
structurally conserved sequences, and hence are crucial for estimating long
distances. We introduce a codon- level model of coding sequence evolution
in which position-specific amino acid frequencies are free parameters. In
our implementation, these are estimated from an alignment using methods
described previously. We use simulations to demonstrate the importance and
feasibility of modeling such behavior; our model produces linear distance
estimates over a wide range of distances, while several alternative models
underestimate long distances relative to short distances. Site-to-site
differences in rates, as well as synonymous/nonsynonymous and
first/second/third-codon-position differences, arise as a natural
consequence of the site-to-site differences in amino acid frequencies.
相似文献
62.
Zhenli Sun Yahong Lu Hao Zhang Dhiraj Kumar Bo Liu Yongchang Gong Min Zhu Liyuan Zhu Zi Liang Sulan Kuang Fei Chen Xiaolong Hu Guangli Cao Renyu Xue Chengliang Gong 《PloS one》2016,11(1)
The gut microbiota has a crucial role in the growth, development and environmental adaptation in the host insect. The objective of our work was to investigate the microbiota of the healthy silkworm Bombyx mori gut and changes after the infection of B. mori cypovirus (BmCPV). Intestinal contents of the infected and healthy larvae of B. mori of fifth instar were collected at 24, 72 and 144 h post infection with BmCPV. The gut bacteria were analyzed by pyrosequencing of the 16S rRNA gene. 147(135) and 113(103) genera were found in the gut content of the healthy control female (male) larvae and BmCPV-infected female (male) larvae, respectively. In general, the microbial communities in the gut content of healthy larvae were dominated by Enterococcus, Delftia, Pelomonas, Ralstonia and Staphylococcus, however the abundance change of each genus was depended on the developmental stage and gender. Microbial diversity reached minimum at 144 h of fifth instar larvae. The abundance of Enterococcus in the females was substantially lower and the abundance of Delftia, Aurantimonas and Staphylococcus was substantially higher compared to the males. Bacterial diversity in the intestinal contents decreased after post infection with BmCPV, whereas the abundance of both Enterococcus and Staphylococcus which belongs to Gram-positive were increased. Therefore, our findings suggested that observed changes in relative abundance was related to the immune response of silkworm to BmCPV infection. Relevance analysis of plenty of the predominant genera showed the abundance of the Enterococcus genus was in negative correlation with the abundance of the most predominant genera. These results provided insight into the relationship between the gut microbiota and development of the BmCPV-infected silkworm. 相似文献
63.
Jing Peng Hong Xu Bei Yang Jia Hu Bao-Ping Zhang Lin Zou Hai-Bin Kuang 《Peptides》2010,31(12):2255-2258
The menopause, defined as the permanent cessation of menstruation resulting from ovarian failure, is characterized by elevated levels of serum gonadotropins. Recent studies have demonstrated that the gonadotropin hypersecretion in postmenopausal women is secondary to increase of KiSS-1 mRNA from the hypothalamus neurons, which encoded kisspeptin peptides. The present study was designed to determine whether plasma kisspeptins levels are altered in postmenopausal women. Blood samples were taken from 145 postmenopausal women, 35 young women and 30 pregnant women control in the first trimester. The plasma concentration of kisspeptins, follicle-stimulating hormone (FSH), luteinizing hormone (LH) and estradiol (E2) was measured using immunoassay kits. Results indicated that plasma kisspeptins levels in postmenopausal women had higher than those in young women (5.25 ± 0.36; 4.48 ± 0.34 pmol/L), but no significant difference was found between the two groups (p = 0.179). Plasma FSH and LH levels were significantly higher in postmenopausal women (124.67 ± 12.78, 57.14 ± 3.57 mIu/mL) than those in young women (9.23 ± 2.78, 7.56 ± 2.71 mIu/mL, p < 0.001). However, Plasma kisspeptins levels were not significantly correlated to FSH and LH in postmenopausal women (r = ?0.23, 0.324; p = 0.927, 0.176, respectively), and also there was no any correlation between plasma kisspeptins and E2 in postmenopausal women (r = ?0.065; p = 0.792). Collectively, there was no significant difference in plasma kisspeptins levels between postmenopausal and young women. Our result suggested that kisspeptins’ role during menopause might mainly act in central rather than peripheral system and it could not be currently used as a clinical marker for menopause. 相似文献
64.
Haiyang Zhang Zhe Lin Daoyong Tan Chunhua Liu Yali Kuang Zhu Li 《Biotechnology letters》2017,39(1):79-84
Objectives
To develop a more effective dissolved air flotation process for harvesting microalgae biomass, a co-flocculation/air flotation (CAF) system was developed that uses an ejector followed by a helix tube flocculation reactor (HTFR) as a co-flocculation device to harvest Chlorella sp. 64.01.Results
The optimal size distribution of micro-bubbles and an air release efficiency of 96 % were obtained when the flow ratio of inlet fluid (raw water) to motive fluid (saturated water) of the ejector was 0.14. With a reaction time of 24 s in the HTFR, microalgae cells and micro-bubbles were well flocculated, and these aerated flocs caused a fast rising velocity (96 m/h) and high harvesting efficiency (94 %).Conclusions
In a CAF process, micro-bubbles can be encapsulated into microalgae flocs, which makes aerated flocs more stable. CAF is an effective approach to harvesting microalgae.65.
During cotranslational protein targeting by the Signal Recognition Particle (SRP), the correct cargo accelerates stable complex assembly between the SRP and SRP receptor (FtsY) by several orders of magnitude, thus enabling rapid and faithful cargo delivery to the target membrane. The molecular mechanism underlying this cargo-induced rate acceleration has been unclear. Here we show that the SRP RNA allows assembly of the SRP-FtsY complex to be specifically stimulated by a correct cargo, and, reciprocally, a correct cargo enables the SRP RNA to optimize its electrostatic interactions with FtsY. These results combined with recent structural work led us to suggest a "conformational selection" model that explains the synergistic action of the SRP RNA with the cargo in accelerating complex assembly. In addition to its previously proposed role in preventing the premature dissociation of SRP and FtsY, we found that the SRP RNA also plays an active role in ensuring the formation of productive assembly intermediates, thus guiding the SRP and FtsY through the most efficient pathway of assembly. 相似文献
66.
The excitation energy transfer from light harvesting chlorophyll protein complexes to PS Ⅱ was inhibited under water stress. The contents of iriternal antennae chlorophyll-protein complexes of PS Ⅱ (CPa), light harvesting chlorophyll-protein complexes of PS Ⅱ (LHC Ⅱ ), light harvesting chlorophyll-protein of PS Ⅰ (LHC Ⅰ ) and chlorophyll a protein complex of reaction center of PS Ⅰ were decreased by water stress. The decrease of chlorophyll-protein complexes of PS Ⅱ was greater than that of PS Ⅰ . It was indicated that the amount of 25 kD polypeptide of LHC Ⅱ in particular, as well as that of 43 and 47 kD polypeptides of CPa, and 21 kD polypeptide of LHC Ⅰ , were reduced by water stress. 相似文献
67.
Roshan Joy Martis U. Rajendra Acharya Hari Prasad Chua Kuang Chua Choo Min Lim Jasjit S. Suri 《Biomedical signal processing and control》2013,8(6):888-900
Atrial fibrillation (AF) and atrial flutter (AFL) are the two common atrial arrhythmia encountered in the clinical practice. In order to diagnose these abnormalities the electrocardiogram (ECG) is widely used. The conventional linear time and frequency domain methods cannot decipher the hidden complexity present in these signals. The ECG is inherently a non-linear, non-stationary and non-Gaussian signal. The non-linear models can provide improved results and capture minute variations present in the time series. Higher order spectra (HOS) is a non-linear dynamical method which is highly rugged to noise. In the present study, the performances of two methods are compared: (i) 3rd order HOS cumulants and (ii) HOS bispectrum. The 3rd order cumulant and bispectrum coefficients are subjected to dimensionality reduction using independent component analysis (ICA) and classified using classification and regression tree (CART), random forest (RF), artificial neural network (ANN) and k-nearest neighbor (KNN) classifiers to select the best classifier. The ICA components of cumulant coefficients have provided the average accuracy, sensitivity, specificity and positive predictive value of 99.50%, 100%, 99.22% and 99.72% respectively using KNN classifier. Similarly, the ICA components of HOS bispectrum coefficients have yielded the average accuracy, sensitivity, specificity and PPV of 97.65%, 98.16%, 98.75% and 99.53% respectively using KNN. So, the ICA performed on the 3rd order HOS cumulants coupled with KNN classifier performed better than the HOS bispectrum method. The proposed methodology is robust and can be used in mass screening of cardiac patients. 相似文献
68.
An all-electron scalar relativistic calculation was performed on Au
n
H2O (n = 1–13) clusters using density functional theory (DFT) with the generalized gradient approximation at PW91 level. The calculation
results reveal that, after adsorption, the small gold cluster would like to bond with oxygen and the H2O molecule prefers to occupy the single fold coordination site. Reflecting the strong scalar relativistic effect, Au
n
geometries are distorted slightly but still maintain a planar structure. The Au–Au bond is strengthened and the H–O bond
is weakened, as manifested by the shortening of the Au–Au bond-length and the lengthening of the H–O bond-length. The H–O–H
bond angle becomes slightly larger. The enhancement of reactivity of the H2O molecule is obvious. The Au–O bond-lengths, adsorption energies, VIPs, HLGs, HOMO (LUMO) energy levels, charge transfers
and the highest vibrational frequencies of the Au–O mode for Au
n
H2O clusters exhibit an obvious odd-even oscillation. The most favorable adsorption between small gold clusters and the H2O molecule takes place when the H2O molecule is adsorbed onto an even-numbered Au
n
cluster and becomes an Au
n
H2O cluster with an even number of valence electrons. The odd–even alteration of magnetic moments is observed in Au
n
H2O clusters and may serve as material with a tunable code capacity of “0” and “1” by adsorbing a H2O molecule onto an odd or even-numbered small gold cluster. 相似文献
69.
Jyh‐Hong Lee Yuan‐Ta Shih Ming‐Liang Wei Chi‐Kuang Sun Bor‐Luen Chiang 《Journal of biophotonics》2019,12(5)
Atopic dermatitis (AD) is a cutaneous disease resulting from a defective barrier and dysregulated immune response. The severity scoring of atopic dermatitis (SCORAD) is used to classify AD. Noninvasive imaging approaches supplementary to SCORAD were investigated. Cr:forsterite laser‐based microscopy was employed to analyze endogenous third‐harmonic generation (THG) and second‐harmonic generation (SHG) signals from skin. Imaging parameters were compared between different AD severities. Three‐dimensional reconstruction of imaged skin layers was performed. Finally, statistic models from quantitative imaging parameters were developed for predicting disease severity. Our data demonstrate that THG signal intensity of lesional skin in AD were significantly increased and was positively correlated with AD severity. Characteristic gray level co‐occurrence matrix (GLCM) values were observed in more severe AD. In the 3D reconstruction video, individual dermal papilla and obvious fibrosis in the upper papillary dermis were easily identified. Our estimation models could predict the disease severity of AD patients with an accuracy of nearly 85%. The THG signal intensity and characteristic GLCM patterns are associated with AD severity and can serve as quantitative predictive parameters. Our imaging approach can be used to identify the histopathological changes of AD objectively, and to complement the SCORAD index, thus improving the accuracy of classifying AD severity. 相似文献
70.
Suurmond J Dorjée AL Boon MR Knol EF Huizinga TW Toes RE Schuerwegh AJ 《Arthritis research & therapy》2011,13(5):R150