Search

A 12-week feeding trial was conducted to evaluate the effects of replacing fish meal by chicken haemoglobin powder in largemouth bass diets. Four isonitrogenous (48%) and isolipidic (12%) diets were formulated to replace 0% (control), 9.80%, 19.61% and 29.41% of fish meal with chicken haemoglobin powder. Each diet was fed to triplicate groups of fish (initial weight: 49.50 ± 0.07 g) twice daily. The fish specific growth rate was significantly reduced when diet replacement level was up to 19.61%, which may be related to the feed intake and apparent digestibility coefficient of protein and amino acids. Meanwhile, the feed efficiency ratio and protein efficiency ratio were not significantly decreased until the replacement level up to 29.41%. The activity of CCP was significantly reduced when 19.61% of fish meal was replaced. Meanwhile, the activity of lysozyme and serum protein content was significantly altered in fish fed with the diets up to 29.41% replacement. Additionally, the red blood cell count and haemoglobin content was significantly decreased when the replacement level was up to 19.61%. In overall, the diet with 9.80% of chicken haemoglobin powder was more suitable for largemouth bass.

Increasing evidence has indicated that prolonged use of anti-VEGF (vascular endothelial growth factor) agents for cancer therapy promotes tumor resistance. To gain insight into the molecular mechanism underlying resistance to anti-VEGF therapy, we developed a mouse Lewis lung carcinoma (LLC) cell line that is resistant to treatment with a potent VEGF inhibitor, VEGF-Trap, through repeated in vivo selection. We compared the transcriptome profiles of resistant and non-resistant tumor cells using RNA-seq analysis. VEGF-C was significantly up-regulated in resistant tumor cells, as determined by quantitative real-time PCR and immunohistochemical analyses. Inhibition of VEGF-C in resistant cells suppressed endothelial cell migration in vitro and partially restored sensitivity to VEGF-Trap treatment in vivo. Our findings indicate that tumors may develop resistance to anti-VEGF therapy by activating the VEGF-C pathway.

Trypanosoma brucei is a unicellular flagellated eukaryotic parasite that causes African trypanosomiasis in human and domestic animals with devastating health and economic consequences. Recent studies have revealed the important roles of the single flagellum of T. brucei in many aspects, especially that the flagellar motility is required for the viability of the bloodstream form T. brucei, suggesting that impairment of the flagellar function may provide a promising cure for African sleeping sickness. Knowing the flagellum proteome is crucial to study the molecular mechanism of the flagellar functions. Here we present a novel computational method for identifying flagellar proteins in T. brucei, called trypanosome flagellar protein predictor (TFPP). TFPP was developed based on a list of selected discriminating features derived from protein sequences, and could predict flagellar proteins with ∼92% specificity at a ∼84% sensitivity rate. Applied to the whole T. brucei proteome, TFPP reveals 811 more flagellar proteins with high confidence, suggesting that the flagellar proteome covers ∼10% of the whole proteome. Comparison of the expression profiles of the whole T. brucei proteome at three typical life cycle stages found that ∼45% of the flagellar proteins were significantly changed in expression levels between the three life cycle stages, indicating life cycle stage-specific regulation of flagellar functions in T. brucei. Overall, our study demonstrated that TFPP is highly effective in identifying flagellar proteins and could provide opportunities to study the trypanosome flagellar proteome systematically. Furthermore, the web server for TFPP can be freely accessed at http:/wukong.tongji.edu.cn/tfpp.

Nucleosome occupancy results in complex sequence variation rate heterogeneity by either increasing mutation rate or inhibiting DNA repair in yeast, fish, and human. H2A.Z nucleosome is extensively involved in gene transcription activation and regulation. To test whether H2A.Z nucleosome has the similar impact on sequence variability in the Drosophila genome, we profiled the H2A.Z nucleosome occupancy and sequence variation rate at gene ends and splicing sites. Consistent with previous studies, H2A.Z nucleosome positioning helps to demarcate the borders of exons. Nucleosome occupancy is anticorrelated with sequence divergence rate in the regions flanking transcription start sites and splicing sites. However, there is no rate heterogeneity between the linker DNA and H2A.Z nucleosomal DNA regardless of nucleosome occupancy, fuzziness, positioning in promoter, coding, and intergenic regions, young or old genes. But the rate at intergenic nucleosomes and the flanking linker regions is higher than that at the genic counterparts. Further analyses found that the high sequence divergence rate in the promoter regions that are usually nucleosome depleted regions may be likely resulted from the high mutation rate in the enriched tandem repeats. Interestingly, within nucleosomes spanning splicing sites, sequence variability of nucleosomal DNA significantly increases from the end within exons to the other end protruding into introns. The relaxed functional constraint in introns contributes to the high rate of nucleosomal DNA residing in introns while the strict functional constraint in exons maintains the low rate of nucleosomal DNA residing in exons. Taken together, H2A.Z nucleosome occupancy has no effect on sequence variability of Drosophila genome, which is likely determined by local sequence composition and the concomitant selection pressure.

Despite overt clinical success of anti-VEGF (vascular endothelial growth factor) agents, such as Avastin, for cancer patients, increasing evidence shows that prolonged treatment of anti-VEGF therapy results in tumor resistance. In order to understand how tumor cells become resistant to anti-VEGF therapy, we developed a mouse Lewis lung carcinoma (LLC) cell line, which was resistant to a potent VEGF blocker, VEGF-Trap. The cell line was established through five rounds of VEGF-Trap treatment and selection in vivo. In each round, C57BL/6 mice were inoculated with LLC cells and subjected to VEGF-Trap or PBS treatment. Tumors grown from treated mice were harvested and the isolated cells were injected to a new batch of mice for the next round of treatment. It was found that tumor cells became insensitive to VEGF-Trap in vivo after five rounds of VEGF-Trap treatment, i.e., VEGF-Trap no longer inhibited tumor growth. In contrast, VEGF-Trap remained efficacious to the LLC cells which underwent five passages in mice but treated with PBS. The resistance phenotype was maintained in LLC cells after the tumor cells were expanded for a number of passages in vitro, indicating that the resistance was due to inherited alterations in tumor cells. To gain insights into the molecular mechanism underlying the resistance to anti-VEGF therapy, we compared transcriptome profiles of the resistant and non-resistant tumor cells using mRNA-seq. The next generation sequencing reads were aligned to mouse genome; gene transcripts were assembled and calculated for relative abundance for individual gene. Results showed that 644 genes were differentially expressed with statistically significances, 317 up-regulated and 327 down-regulated in the resistant tumor cells. Interestingly, VEGF-C was significantly up-regulated in the resistant tumor cells (fold change = 4.91), which was further verified by real-time PCR analysis. Given the stimulatory effects of VEGF-C on both angiogenesis and lymphatic angiogenesis, it is possible that VEGF-C over-expression plays a role in the development of LLC tumor resistance to anti-VEGF therapy. Citation Format: Dong Li, Kun Xie, Guitao Ding, Hongwen Li, Xuejing Yao, Cizhong Jiang, Jianmin Fang. Transcriptome analyses of the tumor cell line resistant to anti-VEGF therapy. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1611. doi:10.1158/1538-7445.AM2013-1611

Background Nucleosome organization determines the chromatin state, which in turn controls gene expression or silencing. Nucleosome remodeling occurs during somatic cell reprogramming, but it is still unclear to what degree the re-established nucleosome organization of induced pluripotent stem cells (iPSCs) resembles embryonic stem cells (ESCs), and whether the iPSCs inherit some residual gene expression from the parental fibroblast cells. Results We generated genome-wide nucleosome maps in mouse ESCs and in iPSCs reprogrammed from somatic cells belonging to three different germ layers using a secondary reprogramming system. Pairwise comparisons showed that the nucleosome organizations in the iPSCs, regardless of the iPSCs’ tissue of origin, were nearly identical to the ESCs, but distinct from mouse embryonic fibroblasts (MEF). There is a canonical nucleosome arrangement of -1, nucleosome depletion region, +1, +2, +3, and so on nucleosomes around the transcription start sites of active genes whereas only a nucleosome occupies silent transcriptional units. Transcription factor binding sites possessed characteristic nucleosomal architecture, such that their access was governed by the rotational and translational settings of the nucleosome. Interestingly, the tissue-specific genes were highly expressed only in the parental somatic cells of the corresponding iPS cell line before reprogramming, but had a similar expression level in all the resultant iPSCs and ESCs. Conclusions The re-established nucleosome landscape during nuclear reprogramming provides a conserved setting for accessibility of DNA sequences in mouse pluripotent stem cells. No persistent residual expression program or nucleosome positioning of the parental somatic cells that reflected their tissue of origin was passed on to the resulting mouse iPSCs. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0109-x) contains supplementary material, which is available to authorized users.