iDNA-Methyl: Identifying DNA methylation sites via pseudo trinucleotide composition

Predominantly occurring on cytosine, DNA methylation is a process by which cells can modify their DNAs to change the expression of gene products. It plays very important roles in life development but also in forming nearly all types of cancer. Therefore, knowledge of DNA methylation sites is significant for both basic research and drug development. Given an uncharacterized DNA sequence containing many cytosine residues, which one can be methylated and which one cannot? With the avalanche of DNA sequences generated during the postgenomic age, it is highly desired to develop computational methods for accurately identifying the methylation sites in DNA. Using the trinucleotide composition, pseudo amino acid components, and a dataset-optimizing technique, we have developed a new predictor called “iDNA-Methyl” that has achieved remarkably higher success rates in identifying the DNA methylation sites than the existing predictors. A user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/iDNA-Methyl, where users can easily get their desired results. We anticipate that the web-server predictor will become a very useful high-throughput tool for basic research and drug development and that the novel approach and technique can also be used to investigate many other DNA-related problems and genome analysis.     

All members in the sphingomyelin synthase gene family have ceramide phosphoethanolamine synthase activity

Sphingomyelin synthase-related protein (SMSr) synthesizes the sphingomyelin analog ceramide phosphoethanolamine (CPE) in cells. Previous cell studies indicated that SMSr is involved in ceramide homeostasis and is crucial for cell function. To further examine SMSr function in vivo, we generated Smsr KO mice that were fertile and had no obvious phenotypic alterations. Quantitative MS analyses of plasma, liver, and macrophages from the KO mice revealed only marginal changes in CPE and ceramide as well as other sphingolipid levels. Because SMS2 also has CPE synthase activity, we prepared Smsr/Sms2 double KO mice. We found that CPE levels were not significantly changed in macrophages, suggesting that CPE levels are not exclusively dependent on SMSr and SMS2 activities. We then measured CPE levels in Sms1 KO mice and found that Sms1 deficiency also reduced plasma CPE levels. Importantly, we found that expression of Sms1 or Sms2 in SF9 insect cells significantly increased not only SM but also CPE formation, indicating that SMS1 also has CPE synthase activity. Moreover, we measured CPE synthase K_m and V_max for SMS1, SMS2, and SMSr using different NBD ceramides. Our study reveals that all mouse SMS family members (SMSr, SMS1, and SMS2) have CPE synthase activity. However, neither CPE nor SMSr appears to be a critical regulator of ceramide levels in vivo.     

阳离子脂质体介导RNA干扰的效果评价

考察自制的肽型阳离子脂质体CDO14作为RNA转染载体的细胞毒性及其运载si RNA进行RNA干扰的效果。通过MTT法检测脂质体对稳定表达荧光素酶的肺癌A549(Luc-A549)细胞的毒性。以脂质体为载体将荧光素酶si RNA(Luc-si RNA)转染至Luc-A549细胞内,用发光仪检测转染细胞内荧光素酶含量,BCA法检测细胞内总蛋白含量。在裸鼠腋下接种Luc-A549细胞,成瘤后尾静脉注射Luc-si RNA和脂质体的复合物,利用活体成像系统检测模型小鼠体内荧光素酶的表达量。细胞毒性实验表明,自制脂质体的毒性与商品脂质体DOTAP相近,低于商品脂质体Lipo2000;细胞转染实验表明自制脂质体作为基因转染载体的转染效率高于DOTAP;体内转染实验表明CDO14作为载体转染效果优于DOTAP。结果表明,肽型阳离子脂质体CDO14具有毒性小、转染效率高等优点,有望作为转染载体用于基因治疗。     

Update of ichthyofauna diversity and ecological status of a coastal River Nero (Côte d’Ivoire – West Africa)

The general aim of this study is to update the inventory of the fish species and to specify distribution patterns in the Nero River ichthyofauna in order to establish some basis for the conservation of these fish communities and their habitat. From February 2009 to January 2010, thirty-three sites were sampled monthly with gill nets and a backpack electrofisher, and environmental variables were recorded. Overall, 46 species included in 33 genuses, 24 families and 9 orders were collected. Eleven families and 30 species were the first records for the Nero River. Including all species previously listed in the literature, the number of species presently known in the Nero River and its tributaries is revised to 59. Four families, Alestidae (21%), Schilbeidae (19%), Cyprinidae (17%) and Cichlidae (16%) that made up 73% of the total number of the catches, were the most dominant. The most dominant numerical species were Schilbe mandibularis and Brycinus longipinnis. Fish species and sampling sites along with eight environmental variables were ordinated with canonical correspondence analysis (CCA) coupled to the Monte Carlo test. Ecological status based on fish assemblage according to environmental variables and anthropogenic pressures showed that miss dead wood leaves and roots, electrical conductivity, total dissolved solids, mud, nitrite, basin width, dissolved oxygen and pH, were the primary factors influencing fish distribution. The environmental tolerance index (ETI), ecological tolerance (t_k) and optima (u_k) values of 10 species to 8 different environmental variables were analyzed. Six species (Hemichromis fasciatus, Epiplatys chaperi, Barbus ablabes, B. longipinnis, Hemichromis bimaculatus and Chromidotilapia guntheri) have high ETI and a cosmopolitan distribution in the Nero River. In the tributaries of the middle course, high concentrations of nitrite in the water, added to the presence of a lot of tolerant species in the ichthyofauna are indications of disturbance of these areas. Subsequent recommendations were formulated for efficient restoration and conservation management of this River.     

SNP identification and marker assay development for high-throughput selection of soybean cyst nematode resistance

Background

Soybean cyst nematode (SCN) is the most economically devastating pathogen of soybean. Two resistance loci, Rhg1 and Rhg4 primarily contribute resistance to SCN race 3 in soybean. Peking and PI 88788 are the two major sources of SCN resistance with Peking requiring both Rhg1 and Rhg4 alleles and PI 88788 only the Rhg1 allele. Although simple sequence repeat (SSR) markers have been reported for both loci, they are linked markers and limited to be applied in breeding programs due to accuracy, throughput and cost of detection methods. The objectives of this study were to develop robust functional marker assays for high-throughput selection of SCN resistance and to differentiate the sources of resistance.

Results

Based on the genomic DNA sequences of 27 soybean lines with known SCN phenotypes, we have developed Kompetitive Allele Specific PCR (KASP) assays for two Single nucleotide polymorphisms (SNPs) from Glyma08g11490 for the selection of the Rhg4 resistance allele. Moreover, the genomic DNA of Glyma18g02590 at the Rhg1 locus from 11 soybean lines and cDNA of Forrest, Essex, Williams 82 and PI 88788 were fully sequenced. Pairwise sequence alignment revealed seven SNPs/insertion/deletions (InDels), five in the 6th exon and two in the last exon. Using the same 27 soybean lines, we identified one SNP that can be used to select the Rhg1 resistance allele and another SNP that can be employed to differentiate Peking and PI 88788-type resistance. These SNP markers have been validated and a strong correlation was observed between the SNP genotypes and reactions to SCN race 3 using a panel of 153 soybean lines, as well as a bi-parental population, F₅–derived recombinant inbred lines (RILs) from G00-3213 x LG04-6000.

Conclusions

Three functional SNP markers (two for Rhg1 locus and one for Rhg4 locus) were identified that could provide genotype information for the selection of SCN resistance and differentiate Peking from PI 88788 source for most germplasm lines. The robust KASP SNP marker assays were developed. In most contexts, use of one or two of these markers is sufficient for high-throughput marker-assisted selection of plants that will exhibit SCN resistance.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1531-3) contains supplementary material, which is available to authorized users.     

A comparison of membranes and enrichment strategies for microbial fuel cells

The external resistance is perhaps the easiest way to influence the operation of a microbial fuel cell (MFC). In this paper, three enrichment strategies, whereby the external resistance was fixed at: (1) a high value in order to maximize the cell voltage (U strategy); (2) a low value in order to maximize the current (I strategy); and (3) a value equal to the internal resistance of the MFC to maximize the power output (P strategy), were investigated. The I strategy resulted in increased maximum power generation and the likely reason is that electron transfer was facilitated under low external resistance, which in turn, favored the development of an electrochemically active biofilm. This experiment was conducted in a single-chamber MFC system equipped with a membrane electrode assembly, and a comparison of the performance achieved by five different membranes is also provided. Selemion was found to be a suitable alternative to Nafion.     

Low-carbon assessment for ecological wastewater treatment by a constructed wetland in Beijing

Presented in this paper is a low-carbon assessment for wastewater treatment by a constructed wetland as ecological engineering. Systems accounting by combining process and input-output analyses is applied to track both direct and indirect GHG emissions associated with the wastewater treatment. Based on the detailed assessment procedures and the embodied GHG emission intensity database for the Chinese economy in 2007, the GHG emissions embodied in both the construction and operation stages of a pilot constructed wetland in Beijing are investigated in concrete detail, with parallel calculations carried out for a cyclic activated sludge plant as a typical conventional wastewater treatment system for comparison. With the overall embodied GHG emissions taken into account, the constructed wetland is shown to be remarkably less carbon intensive than the conventional wastewater treatment system, and the contrast in GHG emission structure is also revealed and characterized. According to the results, the ecological engineering of the constructed wetland is considered to be favorable for achieving the low-carbon goal.     

Differential impact of caveolae and caveolin-1 scaffolds on the membrane raft proteome

Caveolae, a class of cholesterol-rich lipid rafts, are smooth invaginations of the plasma membrane whose formation in nonmuscle cells requires caveolin-1 (Cav1). The recent demonstration that Cav1-associated cavin proteins, in particular PTRF/cavin-1, are also required for caveolae formation supports a functional role for Cav1 independently of caveolae. In tumor cells deficient for Golgi β-1,6N-acetylglucosaminyltransferase V (Mgat5), reduced Cav1 expression is associated not with caveolae but with oligomerized Cav1 domains, or scaffolds, that functionally regulate receptor signaling and raft-dependent endocytosis. Using subdiffraction-limit microscopy, we show that Cav1 scaffolds are homogenous subdiffraction-limit sized structures whose size distribution differs from that of Cav1 in caveolae expressing cells. These cell lines displaying differing Cav1/caveolae phenotypes are effective tools for probing the structure and composition of caveolae. Using stable isotope labeling by amino acids in cell culture, we are able to quantitatively distinguish the composition of caveolae from the background of detergent-resistant membrane proteins and show that the presence of caveolae enriches the protein composition of detergent-resistant membrane, including the recruitment of multiple heterotrimeric G-protein subunits. These data were further supported by analysis of immuno-isolated Cav1 domains and of methyl-β-cyclodextrin-disrupted detergent-resistant membrane. Our data show that loss of caveolae results in a dramatic change to the membrane raft proteome and that this change is independent of Cav1 expression. The proteomics data, in combination with subdiffraction-limit microscopy, indicates that noncaveolar Cav1 domains, or scaffolds are structurally and functionally distinct from caveolae and differentially impact on the molecular composition of lipid rafts.     

Mastication and the postorbital ligament: dynamic strain in soft tissues

Although the FEED database focuses on muscle activity patterns, it is equally suitable for other physiological recording and especially for synthesizing different types of information. The present contribution addresses the interaction between muscle activity and ligamentary stretch during mastication. The postorbital ligament is the thickened edge of a septum dividing the orbital contents from the temporal fossa and is continuous with the temporal fascia. As a tensile element, this fascial complex could support the zygomatic arch against the pull of the masseter muscle. An ossified postorbital bar has evolved repeatedly in mammals, enabling resistance to compression and shear in addition to tension. Although such ossification clearly reinforces the skull against muscle pull, the most accepted explanation is that it helps isolate the orbital contents from contractions of the temporalis muscle. However, it has never been demonstrated that the contraction of jaw muscles deforms the unossified ligament. We examined linear deformation of the postorbital ligament in minipigs, Sus scrofa, along with electromyography of the jaw muscles and an assessment of changes in pressure and shape in the temporalis. During chewing, the ligament elongated (average 0.9%, maximum 2.8%) in synchrony with the contraction of the elevator muscles of the jaw. Although the temporalis bulged outward and created substantial pressure against the braincase, the superficial fibers usually retracted caudally, away from the postorbital ligament. In anesthetized animals, stimulating either the temporalis or the masseter muscle in isolation usually elongated the ligament (average 0.4-0.7%). These results confirm that contraction of the masticatory muscles can potentially distort the orbital contents and further suggest that the postorbital ligament does function as a tension member resisting the pull of the masseter on the zygomatic arch.