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.     

乐至黑山羊PRLR基因外显子10多态性与产羔数的关系研究

设计2对特异性引物对乐至黑山羊PRLR基因第10外显子进行了PCR-SSCP检测,并研究该基因与产子性能的相关性。结果表明,P1引物扩增片段不存在多态性;P2引物扩增片段存在多态性,表现为AA,AB,AD和CD 4种基因型,测序结果表明,4种基因型都在该片段第89、94、146和157位存在C→T、A→C、C→G、G→C的突变;此外AA型还在61位发生C→T的突变;AD型还在175位发生A→G的突变;CD型还在24位发生T→C的突变,96位发生C→T的突变,通过统计分析发现AD型平均产羔数优于其他3种基因型,并且与AB型差异达到显著水平(P<0.05)。因此认为PRLR基因对于乐至黑山羊产子性能有一定的影响。     

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.     

重组人VEGF165的表达纯化及单抗的初步筛选

血管内皮细胞生长因子(vascular endothelial growth factor, VEGF)是抑制肿瘤生长和转移的重要靶点。为获得抗VEGF单抗细胞株,构建了rhVEGF₁₆₅工程菌,并利用复合自动诱导获得高效表达。经纯化获得高纯度rhVEGF₁₆₅蛋白,经检测具有促人脐静脉内皮细胞(human umbilical vein endothelial cells, HUVECs)增殖活性,其EC₅₀为2.4ng/ml。免疫小鼠,获得了3株能稳定分泌抗VEGF单抗的杂交瘤细胞株,为开发VEGF治疗性单抗提供了重要基础。     

CD8+ T cells and IFN-γ mediate the time-dependent accumulation of infected red blood cells in deep organs during experimental cerebral malaria

Background

Infection with Plasmodium berghei ANKA (PbA) in susceptible mice induces a syndrome called experimental cerebral malaria (ECM) with severe pathologies occurring in various mouse organs. Immune mediators such as T cells or cytokines have been implicated in the pathogenesis of ECM. Red blood cells infected with PbA parasites have been shown to accumulate in the brain and other tissues during infection. This accumulation is thought to be involved in PbA–induced pathologies, which mechanisms are poorly understood.

Methods and Findings

Using transgenic PbA parasites expressing the luciferase protein, we have assessed by real-time in vivo imaging the dynamic and temporal contribution of different immune factors in infected red blood cell (IRBC) accumulation and distribution in different organs during PbA infection. Using deficient mice or depleting antibodies, we observed that CD8⁺ T cells and IFN-γ drive the rapid increase in total parasite biomass and accumulation of IRBC in the brain and in different organs 6–12 days post-infection, at a time when mice develop ECM. Other cells types like CD4⁺ T cells, monocytes or neutrophils or cytokines such as IL-12 and TNF-α did not influence the early increase of total parasite biomass and IRBC accumulation in different organs.

Conclusions

CD8⁺ T cells and IFN-γ are the major immune mediators controlling the time-dependent accumulation of P. berghei-infected red blood cells in tissues.     

OAS1蛋白单克隆抗体的制备及其表征

目的:用OAS1蛋白免疫小鼠,获得OAS1特异性单克隆抗体,为OAS1的含量测定提供基础。方法:通过全基因合成的方法获得目的基因序列,转化大肠杆菌BL21细胞诱导His-OAS1及OAS1蛋白表达,纯化后用作抗原免疫小鼠,取脾融合,筛选稳定分泌抗体的阳性细胞株,制备并纯化单抗,通过SDS-PAGE,ELISA,Western blot等方法进行检测。结果:体外高效表达OAS1蛋白,并成功制备特异性单克隆抗体,效价在5×10^-11mol/L以上,亲和常数为3.37×10⁸ L·mol^-1。结论:获得高亲和力OAS1单克隆抗体,为其含量的检测奠定了基础。     

csd alleles in the red dwarf honey bee (Apis florea,Hymenoptera: Apidae) show exceptionally high nucleotide diversity

Abstract The single locus complementary sex determination (sl‐csd) gene is the primary gene determining the gender of honey bees (Apis spp.). While the csd gene has been well studied in the Western honey bee (Apis mellifera), and comparable data exist in both the Eastern honey bee (Apis cerana) and the giant honey bee (Apis dorsata), no studies have been conducted in the red dwarf honey bee, Apis florea. In this study we cloned the genomic region 3 of the A. florea csd gene from 60 workers, and identified 12 csd alleles. Analysis showed that similar to A. mellifera, region 3 of the csd gene contains a RS domain at the N terminal, a proline‐rich domain at the C terminal, and a hypervariable region in the middle. However, the A. florea csd gene possessed a much higher level of nucleotide diversity, compared to A. mellifera, A. cerana and Apis dorsata. We also show that similar to the other three Apis species, in A. florea, nonsynonymous mutations in the csd gene are selectively favored in young alleles.