Import Determinants of Organelle-Specific and Dual Targeting Peptides of Mitochondria and Chloroplasts in Arabidopsis thaliana

Most of the mitochondrial and chloroplastic proteins are synthesized in the cytosol as precursor proteins carrying an N-terminal targeting peptide （TP） directing them specifically to a correct organelle. However, there is a group of proteins that are dually targeted to mitochondria and chloroplasts using an ambiguous N-terminal dual targeting peptide （dTP）. Here, we have investigated pattern properties of import determinants of organelle-specific TPs and dTPs combining mathematical multivariate data analysis （MVDA） with in vitro organellar import studies. We have used large datasets of mitochondrial and chloroplastic proteins found in organellar proteomes as well as manually selected data sets of experimentally confirmed organelle-specific TPs and dTPs from Arabidopsis thaliana. Two classes of organelle-specific TPs could be distinguished by MVDA and potential patterns or periodicity in the amino acid sequence contributing to the separation were revealed, dTPs were found to have intermediate sequence features between the organelle-specific TPs. Interestingly, introducing positively charged residues to the dTPs showed clustering towards the mitochondrial TPs in silico and resulted in inhibition of chloroplast, but not mitochondrial import in in vitro organellar import studies. These findings suggest that positive charges in the N-terminal region of TPs may function as an ＇avoidance signal＇ for the chloroplast import.     

Evolutionary relationships of Pemphigus and allied genera (Hemiptera: Aphididae: Eriosomatinae) and their primary endosymbiont,Buchnera aphidicola

Aphids harbor primary endosymbionts, Buchnera aphidicola, in specialized cells within their body cavities. Aphids and Buchnera have strict mutualistic relationships in nutrition exchange. This ancient association has received much attention from researchers who are interested in endosymbiotic evolution. Previous studies have found parallel phylogenetic relationships between non‐galling aphids and Buchnera at lower taxonomic levels (genus, species). To understand whether relatively isolated habitats such as galls have effect on the parallel relationships between aphids and Buchnera, the present paper investigated the phylogenetic relationships of gall aphids from Pemphigus and allied genera, which induce pseudo‐galls or galls on Populus spp. (poplar) and Buchnera. The molecular phylogenies inferred from three aphid genes (COI, COII and EF‐1α) and two Buchnera genes (gnd, 16S rRNA gene) indicated significant congruence between aphids and Buchnera at generic as well as interspecific levels. Interestingly, both aphid and Buchnera phylogenies supported three main clades corresponding to the galling locations of aphids, namely leaf, the joint of leaf blade and petiole, and branch of the host plant. The results suggest phylogenetic conservatism of gall characters, which indicates gall characters are more strongly affected by aphid phylogeny, rather than host plants.     

Research on the Interstitial Fluid Load Support Characteristics and Start-Up Friction Mechanisms of PVA-HA-Silk Composite Hydrogel

Hydrogel has been extensively studied as an articular cartilage repair and replacement material. PVA-HA-Silk composite hydrogel was prepared by freezing-thawing method in this paper. Mechanical properties were determined by experiments and the friction coefficient of PVA-HA-Silk composite hydrogel against steel ball was verified using micro-tribometer. Finite Element Method （FEM） was used to study the lubrication mechanism of PVA-HA-Silk composite hydrogel and the relation between the interstitial fluid load support and the start-up friction resistance. The results show that the elastic modulus and the permeability are 2.07 MPa and 10^-15m^4N^-1s^-1, respectively, and the start-up friction coefficients of PVA-HA-Silk composite hydrogel are in the range of 0.154）.2 at different contact loads, contact time and sliding speeds. The start-up friction resistance of PVA-HA-Silk composite hydrogel increases with the contact load and contact time. With the increase in sliding speed, the start-up friction resistance of PVA-HA-Silk composite hydrogel decreases. There is an inverse relation between the start-up friction resistance and the interstitial fluid load support. The change of fluid flow with the increase in sliding displacement has an important effect on the interstitial fluid load support and friction resistance. The interstitial fluid load support decreases with the increase in contact load and contact time, while the interstitial fluid load support reinforces with the increase in sliding speed. Moreover, PVA-HA-Silk composite hydrogel has mechanical properties of recovery and self-lubricating.     

血清转化生长因子beta-1 在大鼠放射性肝纤维化中的动态表达 及其相关性研

目的:肝癌的放射治疗可导致放射性肝损伤(RILD)、甚至肝纤维化及肝硬化等并发症的发生,因此寻找较佳的血清标记物对放射性肝纤维化的无创诊断及监测具有重要意义。本文通过建立放射性肝纤维化大鼠模型,检测血清转化生长因子β1(TGF-β1)的动态表达,从而探讨其与放射性肝纤维化严重程度的相关性及其作为血清标记物的诊断价值。方法:雄性SD大鼠40只,随机分为模型组(30只)和对照组(10只)。除对照组外,模型组大鼠右半肝均接受单次6MV X线25Gy照射,于照射2月、4月、6月后,随机抽取10只,酶联免疫吸附法(ELISA)检测血清TGF-β1的表达,同时将大鼠肝组织进行HE染色,观察肝组织病理变化及大鼠肝纤维化程度,将后者与血清TGF-β1值进行相关性分析。结果:在照射第2月、4月、6月后,模型组大鼠血清TGF-β1值(分别为551.03±69.00 ng/L、645.31±109.29 ng/L、737.89±118.11 ng/L)逐渐升高,均明显高于对照组(451.71±51.12 ng/L,P<0.05)。通过相关性分析表明,大鼠血清TGF-β1值与肝纤维化程度正相关(r=0.82,P<0.01)。结论:在放射性肝纤维化发生发展中,TGF-β1随着肝纤维化严重程度增加,其表达亦升高。本研究为放射性肝纤维化严重程度的监测提供了一种新的无创、操作简单的手段,为后续TGF-β1作为血清标记物应用于放射性肝纤维化的临床研究奠定了理论基础。     

Cascade effects of crop species richness on the diversity of pest insects and their natural enemies

Understanding how plant species richness influences the diversity of herbivorous and predatory/parasitic arthropods is central to community ecology.We explore the effects of crop species richness on the diversity of pest insects and their natural enemies.Using data from a four-year experiment with five levels of crop species richness,we found that crop species richness significantly affected the pest species richness,but there were no significant effects on richness of the pests’natural enemies.In contrast,the species richness of pest insects significantly affected their natural enemies.These findings suggest a cascade effect where trophic interactions are strong between adjacent trophic levels,while the interactions between connected but nonadjacent trophic levels are weakened by the intermediate trophic level.High crop species richness resulted in a more stable arthropod community compared with communities in monoculture crops.Our results highlight the complicated cross-trophic interactions and the crucial role of crop diversity in the food webs of agro-ecosystems.     

Identification of differentially accumulating pistil proteins associated with self‐incompatibility of non‐heading Chinese cabbage

Non‐heading Chinese cabbage (Brassica campestris L. ssp. chinensis Makino), an important vegetable crop in China, exhibits a typical sporophytic self‐incompatibility (SI) system. To better understand the mechanism of SI response and identify potential candidate proteins involved in the SI system of this vegetable crop, the proteomic approach was taken to identify differential accumulating pistil proteins. Pistils were collected at 0 h and 2 h after self‐pollination at anthesis in self‐incompatible and compatible lines of non‐heading Chinese cabbage, and total proteins were extracted and separated by two‐dimensional gel electrophoresis (2‐DE). A total of 25 protein spots that displayed differential abundance were identified by matrix‐assisted laser desorption/ionisation‐time of flight mass spectrometry (MALDI–TOF/TOF MS) and peptide mass fingerprinting (PMF). Among them, 22 protein spots were confidently established. The mRNA levels of the corresponding genes were detected by quantitative RT‐PCR. The 22 identified protein spots are involved in energy metabolism (four), protein biosynthesis (three), photosynthesis (six), stress response and defence (five), and protein degradation (four). Among these potential candidate proteins, UDP‐sugar pyrophosphorylase could be involved in sucrose degradation to influence pollen germination and growth. Glutathione S–transferases could be involved in pollen maturation, and affect pollen fertility. Senescence‐associated cysteine protease, which is related to programmed cell death, could be mainly related to self pollen recognition of non‐heading Chinese cabbage. The study will contribute to further investigations of molecular mechanism of sporophytic SI in Brassicaceae.     

An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era

Background

Gene expression microarray has been the primary biomarker platform ubiquitously applied in biomedical research, resulting in enormous data, predictive models, and biomarkers accrued. Recently, RNA-seq has looked likely to replace microarrays, but there will be a period where both technologies co-exist. This raises two important questions: Can microarray-based models and biomarkers be directly applied to RNA-seq data? Can future RNA-seq-based predictive models and biomarkers be applied to microarray data to leverage past investment?

Results

We systematically evaluated the transferability of predictive models and signature genes between microarray and RNA-seq using two large clinical data sets. The complexity of cross-platform sequence correspondence was considered in the analysis and examined using three human and two rat data sets, and three levels of mapping complexity were revealed. Three algorithms representing different modeling complexity were applied to the three levels of mappings for each of the eight binary endpoints and Cox regression was used to model survival times with expression data. In total, 240,096 predictive models were examined.

Conclusions

Signature genes of predictive models are reciprocally transferable between microarray and RNA-seq data for model development, and microarray-based models can accurately predict RNA-seq-profiled samples; while RNA-seq-based models are less accurate in predicting microarray-profiled samples and are affected both by the choice of modeling algorithm and the gene mapping complexity. The results suggest continued usefulness of legacy microarray data and established microarray biomarkers and predictive models in the forthcoming RNA-seq era.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0523-y) contains supplementary material, which is available to authorized users.     

Imbalance of Wnt/Dkk Negative Feedback Promotes Persistent Activation of Pancreatic Stellate Cells in Chronic Pancreatitis

The role of persistent activation of pancreatic stellate cells (PSCs) in the fibrosis associated with chronic pancreatitis (CP) is increasingly being recognized. Recent studies have shown that Wnt signaling is involved in the development of fibrosis in multiple organs, however, the role of specific Wnts in pancreatic fibrosis remains unknown. We investigated the role of Wnt signaling during PSC activation in CP and the effect of β-catenin inhibition and Dickkopf-related protein 1 (Dkk1) restoration on the phenotype of PSCs. CP was induced in mice by repetitive caerulein injection and mouse PSCs were isolated and activated in vitro. The expression of Wnts, β-catenin, secreted frizzled-related proteins (sFRPs) and Dkks was analyzed by quantitative RT-PCR and western blotting. The canonical Wnt signaling pathway was examined by immunofluorescence and western blot detection of nuclear β-catenin expression. The effect of recombinant mouse Dkk-1 (rmDkk-1) on cell proliferation and apoptosis was assessed by flow cytometry, immunofluorescence, immunocytochemistry and Cell Counting Kit-8 (CCK-8) analysis. The expression of β-catenin, collagen1α1, TGFβRII, PDGFRβ and α-SMA in PSCs treated with different concentrations of rmDkk-1 or siRNA against β-catenin was determined by quantitative RT-PCR and western blotting. Wnt2 was the only Wnt whose expression was significantly upregulated in response to PSC activation, and Wnt2 and β-catenin protein levels were significantly increased in the pancreas of CP mice, whereas Dkk-1 expression was evidently decreased. Nuclear β-catenin levels were markedly increased in activated PSCs, and rmDkk-1 suppressed the nuclear translocation of β-catenin and the proliferation and extracellular matrix production of PSCs through the downregulation of PDGFRβ and TGFβRII. Upregulation of Dkk-1 expression increased apoptosis in cultured PSCs. These results indicate that Wnt signaling may mediate the profibrotic effect of PSC activation, and Wnt2/Dkk-1 could be potential therapeutic targets for CP.     

Effect of Acute,Slightly Increased Intra-Abdominal Pressure on Intestinal Permeability and Oxidative Stress in a Rat Model

IntroductionIntra-abdominal hypertension (IAH) is known as a common, serious complication in critically ill patients. Bacterial translocation and permeability changes are considered the pathophysiological bases for IAH-induced enterogenic endotoxemia and subsequent multiorgan failure. Nevertheless, the effects of slightly elevated intra-abdominal pressures (IAPs) on the intestinal mucosa and the associated mechanisms remain unclear.MethodsTo investigate the acute effects of different nitrogen pneumoperitoneum grades on colonic mucosa, male Sprague-Dawley rats were assigned to six groups with different IAPs (0 [control], 4, 8, 12, 16, and 20 mmHg, n = 6/group). During 90 min of exposure, we dynamically monitored the heart rate and noninvasive hemodynamic parameters. After gradual decompression, arterial blood gas analyses were conducted. Thereafter, structural injuries to the colonic mucosa were identified using light microscopy. Colon permeability was determined using the expression of tight junction proteins, combined with fluorescein isothiocyanate dextran (FD-4) absorption. The pro-oxidant-antioxidant balance was determined based on the levels of malondialdehyde (MDA) and antioxidant enzymes.ResultsIAH significantly affected the histological scores of the colonic mucosa, tight junction protein expression, mucosal permeability, and pro-oxidant-antioxidant balance. Interestingly, elevations of IAP that were lower than the threshold for IAH also showed a similar, undesirable effect. In the 8 mmHg group, mild hyponatremia, hypocalcemia, and hypoxemia occurred, accompanied by reduced blood and abdominal perfusion pressures. Mild microscopic inflammatory infiltration and increased MDA levels were also detected. Moreover, an 8-mm Hg IAP markedly inhibited the expression of tight junction proteins, although no significant differences in FD-4 permeability were observed between the 0- and 8-mmHg groups.ConclusionsAcute exposure to slightly elevated IAP may result in adverse effects on intestinal permeability and the pro-oxidant-antioxidant balance. Therefore, in patients with critical illnesses, IAP should be dynamically monitored and corrected, as soon as possible, to prevent intestinal mucosal injury and subsequent gut-derived sepsis.