Improving the prediction of RNA secondary structure by detecting and assessing conserved stems

The prediction of RNA secondary structure can be facilitated by incorporating with comparative analysis of homologous sequences. However, most of existing comparative methods are vulnerable to alignment errors and thus are of low accuracy in practical application. Here we improve the prediction of RNA secondary structure by detecting and assessing conserved stems shared by all sequences in the alignment. Our method can be summarized by: 1) we detect possible stems in single RNA sequence using the so-called position matrix with which some possibly paired positions can be uncovered; 2) we detect conserved stems across multiple RNA sequences by multiplying the position matrices; 3) we assess the conserved stems using the Signal-to-Noise; 4) we compute the optimized secondary structure by incorporating the so-called reliable conserved stems with predictions by RNAalifold program. We tested our method on data sets of RNA alignments with known secondary structures. The accuracy, measured as sensitivity and specificity, of our method is greater than predictions by RNAalifold.     

Cadmium accumulation and its effects on metal uptake in maize (Zea mays L.)

The effects of different concentrations of Cd on growth of maize (Zea mays L.) and metal uptake were investigated. Cd accumulations in roots and shoots and the interactions among other metals (Mn, Fe, Cu and Zn) were analyzed using inductively coupled plasma atomic emission spectrometry (ICP-AES). The concentrations of cadmium chloride (CdCl(2).2.5H2O) used ranged from 10(-4) M to 10(-6) M. Cd had stimulatory effects during the first 5 days on root length of Nongda No. 108 at 10(-6) M and 10(-5) M Cd concentrations. Seedlings exposed to 10(-4) M Cd solution exhibited substantial growth reduction, and root growth even stopped. Root growth of Liyu No. 6 was stimulated at concentrations of 10(-5) M and 10(-6) M Cd during the entire experiment (15 days). Cadmium inhibited root growth of Liyu No. 6 at 10(-4) M Cd after 10 days of treatment. The Cd accumulation in roots and shoots of the two cultivars increased significantly (P < 0.05) with increasing Cd concentration and duration of treatment. Cadmium concentrated mainly in the roots, and small amounts were transferred to shoots. The proportion of Cd in the roots of Nongda No. 108 decreased with increases in Cd concentrations and duration of treatment, except for the group exposed to 10(-4) M Cd. In Liyu No. 6, the proportion of Cd in the root decreased progressively with an increase in Cd concentrations. Liyu No. 6 has a greater ability to remove Cd from solution and accumulate it when compared with Nongda No. 108. Liyu No. 6 can be considered a Cd-hyperaccumulator, according to the current accepted shoot concentration that defines hyperaccumulation as 0.01% (w/w) for cadmium. This cultivar, producing many roots and a high biomass and with great ability to accumulate Cd can play an important role in the treatment of soils stressed by Cd.     

High-capacity purification of His-tagged proteins by affinity membranes containing functionalized polymer brushes

Porous membrane absorbers are attractive for increasing the rate of protein purification, but their binding capacity is low relative to porous beads. Modification of membranes with functionalized polymer brushes, however, can greatly enhance capacity. This work demonstrates that membrane modification with poly(2-hydroxyethyl methacrylate) (PHEMA) brushes derivatized with nitrilotriacetate-Ni2+ (NTA-Ni2+) complexes allows purification of polyhistidine-tagged ubiquitin (HisU) in less than 30 min with a binding capacity of 120 mg of HisU/cm3 of porous alumina membrane. Adsorption isotherms show that saturation of the brushes occurs at HisU concentrations as low as 0.04 mg/mL and that these brushes can bind up to 23 monolayers of HisU. Gel electrophoresis reveals that the purity of eluted HisU is more than 99%, even when the initial feed solution contains 10% bovine serum or a 20-fold excess of BSA. Thus, reusable porous membranes modified by PHEMA-NTA-Ni2+ brushes are attractive candidates for rapid purification of polyhistidine-tagged proteins.     

C1q Protein Binds to the Apoptotic Nucleolus and Causes C1 Protease Degradation of Nucleolar Proteins

In infection, complement C1q recognizes pathogen-congregated antibodies and elicits complement activation. Among endogenous ligands, C1q binds to DNA and apoptotic cells, but whether C1q binds to nuclear DNA in apoptotic cells remains to be investigated. With UV irradiation-induced apoptosis, C1q initially bound to peripheral cellular regions in early apoptotic cells. By 6 h, binding concentrated in the nuclei to the nucleolus but not the chromatins. When nucleoli were isolated from non-apoptotic cells, C1q also bound to these structures. In vivo, C1q exists as the C1 complex (C1qC1r₂C1s₂), and C1q binding to ligands activates the C1r/C1s proteases. Incubation of nucleoli with C1 caused degradation of the nucleolar proteins nucleolin and nucleophosmin 1. This was inhibited by the C1 inhibitor. The nucleoli are abundant with autoantigens. C1q binding and C1r/C1s degradation of nucleolar antigens during cell apoptosis potentially reduces autoimmunity. These findings help us to understand why genetic C1q and C1r/C1s deficiencies cause systemic lupus erythematosus.     

基于PAE编码系统构建的半自然条件下长江江豚行为谱

识别和编制动物行为谱是深入研究动物行为及其与环境复杂关系的基础和前提。本研究于2013年8月至2014年4月以栖息在铜陵淡水豚国家级自然保护区半自然水域的8头长江江豚为研究对象,采用焦点动物取样法和随机动物取样法观察记录了动物行为发生的过程、内容和环境,并以"姿势—动作—环境"(posture-act-environment,PAE)为轴心,以行为的功能为依据,构建了长江江豚的PAE行为谱。共分辨记录了半自然水域长江江豚的8种姿势、33种动作和46种行为,并定性描述了不同行为出现频率与年龄组、性别的关系。该行为谱综合了姿势和环境信息,有助于进一步研究长江江豚的生态与行为、促进长江江豚的保护。     

Brucella suis vaccine strain S2-infected immortalized caprine endometrial epithelial cell lines induce non-apoptotic ER-stress

Brucella, which is regarded as an intracellular pathogen responsible for a zoonotic disease called brucellosis, survives and proliferates within several types of phagocytic and non-phagocytic cells. Brucella infects not only their preferred hosts but also other domestic and wild animal species, inducing abortion and infertility. Therefore, the interaction between uterine cells and Brucella is important for understanding the pathogenesis of this disease. In this study, we describe the Brucella suis vaccine strain S2 (B.suis.S2) infection and replication in the immortalized caprine endometrial epithelial cell line hTERT-EECs and the induced cellular and molecular response modulation in vitro. We found that B.suis S2 was able to infect and replicate to high titers and inhibit the proliferation of EECs and induce non-apoptotic pathways, as determined by B.suis.S2 detection using MTT and acridine orange/ethidium bromide (AO/EB) staining and flow cytometry. We explored the evidence of non-apoptotic pathways using real-time quantitative RT-PCR and by western blot analysis. Finally, we discovered the over-expression of GRP78, ATF4, ATF6, PERK, eIF2α, CHOP, and cytochrome c (Cyt-c) but not IRE1, xbp-1, and caspase-3 in B.suis.S2 (HK)-attacked and B.suis.S2-infected cells, suggesting that the molecular mechanism of ER stress sensor activation by B.suis.S2 is basically concomitant with that by B.suis.S2 (HK) and that ER stress, especially the PERK pathway, plays an important role in the process of B.suis.S2 infecting EEC, which may, in part, explain the role of the uterus in the pathogenesis of B.suis.S2.

Electronic supplementary material

The online version of this article (doi:10.1007/s12192-014-0564-x) contains supplementary material, which is available to authorized users.     

Hollow nitrogen-doped carbon microspheres pyrolyzed from self-polymerized dopamine and its application in simultaneous electrochemical determination of uric acid, ascorbic acid and dopamine

Hollow nitrogen-doped carbon microspheres (HNCMS) as a novel carbon material have been prepared and the catalytic activities of HNCMS-modified glassy carbon (GC) electrode towards the electro-oxidation of uric acid (UA), ascorbic acid (AA) and dopamine (DA) have also been investigated. Comparing with the bare GC and carbon nanotubes (CNTs) modified GC (CNTs/GC) electrodes, the HNCMS modified GC (HNCMS/GC) electrode has higher catalytic activities towards the oxidation of UA, AA and DA. Moreover, the peak separations between AA and DA, and DA and UA at the HNCMS/GC electrode are up to 212 and 136 mV, respectively, which are superior to those at the CNTs/GC electrode (168 and 114 mV). Thus the simultaneous determination of UA, AA and DA was carried out successfully. In the co-existence system of UA, AA and DA, the linear response range for UA, AA and DA are 5-30 μM, 100-1000 μM and 3-75 μM, respectively and the detection limits (S/N = 3) are 0.04 μM, 0.91 μM and 0.02 μM, respectively. Meanwhile, the HNCMS/GC electrode can be applied to measure uric acid in human urine, and may be useful for measuring abnormally high concentration of AA or DA. The attractive features of HNCMS provide potential applications in the simultaneous determination of UA, AA and DA.     

Improved performance of membrane free single-chamber air-cathode microbial fuel cells with nitric acid and ethylenediamine surface modified activated carbon fiber felt anodes

Surface modifications of anode materials are important for enhancing power generation of microbial fuel cell (MFC). Membrane free single-chamber air-cathode MFCs, MFC-A and MFC-N, were constructed using activated carbon fiber felt (ACF) anodes treated by nitric acid and ethylenediamine (EDA), respectively. Experimental results showed that the start-up time to achieve the maximum voltages for the MFC-A and MFC-N was shortened by 45% and 51%, respectively as compared to that for MFC-AT equipped with an unmodified anode. Moreover, the power output of MFCs with modified anodes was significantly improved. In comparison with MFC-AT which had a maximum power density of 1304 mW/m², the MFC-N achieved a maximum power density of 1641 mW/m². The nitric acid-treated anode in MFC-A increased the power density by 58% reaching 2066 mW/m². XPS analysis of the treated and untreated anode materials indicated that the power enhancement was attributable to the changes of surface functional groups.     

Influence of supports on catalytic behavior of nickel catalysts in carbon dioxide reforming of toluene as a model compound of tar from biomass gasification

A series of supported Ni catalysts including Ni/MgO, Ni/γ-Al2O3, Ni/α-Al2O3, Ni/SiO2 and Ni/ZrO2 was tested in CO2 reforming of toluene as a model compound of tar from biomass gasification in a fluidized bed reactor, and characterized by the means of temperature programmed reduction with hydrogen (H2-TPR), XRD, TEM and temperature programmed oxidation (TPO). Combining the characterization results with the performance tests, the activity of catalyst greatly depended on Ni particles size, and the stability was affected by the coke composition. Both of them (Ni particle size and coke composition) were closely related to the interaction between nickel and support which would determine the chemical environment where Ni inhabited. The best catalytic performance was observed on Ni/MgO due to the strong interaction between NiO and MgO via the formation of Ni-Mg-O solid solution, and the highest dispersion of Ni particle in the basic environment.     

Immobilizing bifenthrin on wood for termite control

Termites are world-wide pests causing significant losses to annual and perennial crops, as well as damages to wooden components in buildings. Although various chemical, physical, and biological methods have been explored to prevent termite attack on wooden structures, new guiding principles are still needed for environmental protection. In this study, by combining the effective chemical control of bifenthrin and photo-immobilization technique of biomolecules, we developed chitosan as a carrier to embed bifenthrin, which was then immobilized by ultraviolet treatment on the surface of wood (Cunninghamia lanceolata). The immobilized bifenthrin embedded in the photoactive chitosan was characterized by Fourier transform infrared spectroscopy (FTIR), C.H.N analysis, ultraviolet, and fluorescence measurements. The surface structures and biological activity were examined by scanning electron microscopy (SEM), atomic force microscope (AFM), electron spectroscopy for chemical analysis (ESCA), and bioassays. The results indicated that the immobilized bifenthrin can be well protected from free and non-controlled releasing, and has a long-term stability allowing high efficiency against the termite at a dose of 2.5 ??g/cm². This study provides a novel and environmentally-benign technique for the termite control by photo-immobilizing the bifenthrin-embedded chitosan on the surface of C. lanceolata. This technique may be used in combination with the traditional methods for effective termite control.