Could protein tertiary structure influence mammary transgene expression more than tissue specific codon usage?

Animal mammary glands have been successfully employed to produce therapeutic recombinant human proteins. However, considerable variation in animal mammary transgene expression efficiency has been reported. We now consider whether aspects of codon usage and/or protein tertiary structure underlie this variation in mammary transgene expression

The influence of a first-order antedependence model and hyperparameters in BayesCπ for genomic prediction

Objective The Bayesian first-order antedependence models, which specified single nucleotide polymorphisms (SNP) effects as being spatially correlated in the conventional BayesA/B, had more accurate genomic prediction than their corresponding classical counterparts. Given advantages of BayesCπ over BayesA/B, we have developed hyper-BayesCπ, ante-BayesCπ, and ante-hyper-BayesCπ to evaluate influences of the antedependence model and hyperparameters for vg and s g 2 on BayesCπ. Methods Three public data (two simulated data and one mouse data) were used to validate our proposed methods. Genomic prediction performance of proposed methods was compared to traditional BayesCπ, ante-BayesA and ante-BayesB. Results Through both simulation and real data analyses, we found that hyper-BayesCπ, ante-BayesCπ and ante-hyper-BayesCπ were comparable with BayesCπ, ante-BayesB, and ante-BayesA regarding the prediction accuracy and bias, except the situation in which ante-BayesB performed significantly worse when using a few SNPs and π = 0.95. Conclusion Hyper-BayesCπ is recommended because it avoids pre-estimated total genetic variance of a trait compared with BayesCπ and shortens computing time compared with ante-BayesB. Although the antedependence model in BayesCπ did not show the advantages in our study, larger real data with high density chip may be used to validate it again in the future

Variations of O3O_3 and CO in Summertime at a Rural Site Near Beijing

Large intra-season differences in mixing ratios of CO and $O_3$ were detected at Miyun, a rural site north of Beijing, in summer 2006. Despite an increase in mean daytime mixing ratio of CO from 500 ppbv in June to 700 ppbv in July, mean daytime $O_3$ dropped from 67 ppbv in June to 50 ppbv in July and August. The observed changes in CO and $O_3$ are attributed to the influence of the summer monsoonal circulation that develops over the North China Plain in July. Photochemical production of $O_3$ is reduced as a consequence of increased cloudiness during July and August, as indicated by the strong negative correlation observed between $O_3$ and satellite observations of cloud optical depth, with cloudiness having little effect on CO. The analysis suggests a strategy for emission controls that could be implemented in an economically efficient manner to minimize the frequency of high levels of $O_3$ during summer in Beijing.Engineering and Applied Science

Natural selection and functional diversification of the epidermal growth factor receptorEGFR family in vertebrates

AbstractBackgroundGenes that have been subject to adaptive evolution can produce varying degrees of pathology or differing symptomatology. ErbB family receptor activation will initiate a number of downstream signaling pathways, such as mitogen-activated protein kinase (MAPK), activator of transcription (STAT), the modulation of calcium channels, and so on, all of which lead to aggressive tumor behavior. However, the evolutionary mechanisms operating in the retention of ErbB family genes and the changes in selection pressures are not clear.ResultsSixty-two full-length cDNA sequences from 27 vertebrate species were extracted from the UniProt protein database, NCBI's GenBank and the Ensembl database. The result of phylogenetic analysis showed that the four ErbB family members in vertebrates might be formed by gene duplication. In order to determine the mode of evolution in vertebrates, selection analysis and functional divergence analysis were combined to explain the relationship of the site-specific evolution and functional divergence in the vertebrate ErbB family. Our results indicate that the acceleration of asymmetric evolutionary rates and purifying selection together were the main force for the production of ErbBs, and positive selections were detected in the ErbB family.ConclusionAn evolutional phylogeny of 27 vertebrates was presented in our study; the tree showed that the genes have evolved through duplications followed by purifying selection, except for seven sites, which evolved by positive selection. There was one common site with positive selection and functional divergence. In the process of functional differentiation evolving through gene duplication, relaxed selection may play an important part

Inhibition of highly pathogenic PRRSV replication in MARC-145 cells by artificial microRNAs

<p>Abstract</p> <p>Background</p> <p>Highly pathogenic porcine reproductive and respiratory syndrome (HP-PRRS) has caused large economic losses in swine industry in recent years. However, current antiviral strategy could not effectively prevent and control this disease. In this research, five artificial microRNAs (amiRNAs) respectively targeted towards ORF5 (amirGP5-243, -370) and ORF6 (amirM-82, -217,-263) were designed and incorporated into a miRNA-based vector that mimics the backbone of murine miR-155 and permits high expression of amiRNAs in a GFP fused form mediated by RNA Pol II promoter CMV.</p> <p>Results</p> <p>It was found that amirGP5-370 could effectively inhibit H-PRRSV replication. The amirM-263-M-263, which was a dual pre-amiRNA expression cassette where two amirM-263s were chained, showed stronger virus inhibitory effects than single amirM-263. H-PRRSV replication was inhibited up to 120 hours in the MARC-145 cells which were stably transduced by recombinant lentiviruses (Lenti-amirGP5-370, -amirM-263-M-263). Additionally, efficacious dose of amirGP5-370 and amirM-263 expression did not trigger the innate interferon response.</p> <p>Conclusions</p> <p>Our study is the first attempt to suppress H-PRRSV replication in MARC-145 cells through vector-based and lentiviral mediated amiRNAs targeting GP5 or M proteins coding sequences of PRRSV, which indicated that artificial microRNAs and recombinant lentiviruses might be applied to be a new potent anti-PRRSV strategy.</p

Inhibition of HSP90 attenuates porcine reproductive and respiratory syndrome virus production in vitro

BACKGROUND: Porcine reproductive and respiratory syndrome virus (PRRSV) infection leads to substantial economic losses to the swine industry worldwide. However, no effective countermeasures exist to combat this virus infection so far. The most common antiviral strategy relies on directly inhibiting viral proteins. However, this strategy invariably leads to the emergence of drug resistance due to the error-prone nature of viral ploymerase. Targeting cellular proteins required for viral infection for developing new generation of antivirals is gaining concern. Recently, heat shock protein 90 (HSP90) was found to be an important host factor for the replication of multiple viruses and the inhibition of HSP90 showed significant antiviral effects. It is thought that the inhibition of HSP90 could be a promising broad-range antiviral approach. However, the effects of HSP90 inhibition on PRRSV infection have not been evaluated. In the current research, we tried to inhibit HSP90 and test whether the inhibition affect PRRSV infection. METHODS: We inhibit the function of HSP90 with two inhibitors, geldanamycin (GA) and 17- allylamono-demethoxygeldanamycin (17-AAG), and down-regulated the expression of endogenous HSP90 with specific small-interfering RNAs (siRNAs). Cell viability was measured with alamarBlue. The protein level of viral N was determined by western blotting and indirect immunofluorescence (IFA). Besides, IFA was employed to examine the level of viral double-stranded RNA (dsRNA). The viral RNA copy number and the level of IFN-β mRNA were determined by quantitative real-time PCR (qRT-PCR). RESULTS: Our results indicated that both HSP90 inhibitors showed strong anti-PRRSV activity. They could reduce viral production by preventing the viral RNA synthesis. These inhibitory effects were not due to the activation of innate interferon response. In addition, we observed that individual knockdown targeting HSP90α or HSP90β did not show dramatic inhibitory effect. Combined knockdown of these two isoforms was required to reduce viral infection. CONCLUSIONS: Our results shed light on the possibility of developing potential therapeutics targeting HSP90 against PRRSV infection

Proteome changes of lungs artificially infected with H-PRRSV and N-PRRSV by two-dimensional fluorescence difference gel electrophoresis

<p>Abstract</p> <p>Background</p> <p>Porcine reproductive and respiratory syndrome with PRRS virus (PRRSV) infection, which causes significant economic losses annually, is one of the most economically important diseases affecting swine industry worldwide. In 2006 and 2007, a large-scale outbreak of highly pathogenic porcine reproductive and respiratory syndrome (PRRS) happened in China and Vietnam. However little data is available on global host response to PRRSV infection at the protein level, and similar approaches looking at mRNA is problematic since mRNA levels do not necessarily predict protein levels. In order to improve the knowledge of host response and viral pathogenesis of highly virulent Chinese-type PRRSV (H-PRRSV) and Non-high-pathogenic North American-type PRRSV strains (N-PRRSV), we analyzed the protein expression changes of H-PRRSV and N-PRRSV infected lungs compared with those of uninfected negative control, and identified a series of proteins related to host response and viral pathogenesis.</p> <p>Results</p> <p>According to differential proteomes of porcine lungs infected with H-PRRSV, N-PRRSV and uninfected negative control at different time points using two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and mass spectrometry identification, 45 differentially expressed proteins (DEPs) were identified. These proteins were mostly related to cytoskeleton, stress response and oxidation reduction or metabolism. In the protein interaction network constructed based on DEPs from lungs infected with H-PRRSV, HSPA8, ARHGAP29 and NDUFS1 belonged to the most central proteins, whereas DDAH2, HSPB1 and FLNA corresponded to the most central proteins in those of N-PRRSV infected.</p> <p>Conclusions</p> <p>Our study is the first attempt to provide the complex picture of pulmonary protein expression during H-PRRSV and N-PRRSV infection under the in vivo environment using 2D-DIGE technology and bioinformatics tools, provides large scale valuable information for better understanding host proteins-virus interactions of these two PRRSV strains.</p