Selective genotyping to detect quantitative trait loci affecting multiple traits: interval mapping analysis

 Segregating quantitative trait loci can be detected via linkage to genetic markers. By selectively genotyping individuals with extreme phenotypes for the quantitative trait, the power per individual genotyped is increased at the expense of the power per individual phenotyped, but linear-model estimates of the quantitative-locus effect will be biased. The properties of single- and multiple-trait maximum-likelihood estimates of quantitative-loci parameters derived from selectively genotyped samples were investigated using Monte-Carlo simulations of backcross populations. All individuals with trait records were included in the analyses. All quantitative-locus parameters and the residual correlation were unbiasedly estimated by multiple-trait maximum-likelihood methodology. With single-trait maximum-likelihood, unbiased estimates for quantitative-locus effect and location, and the residual variance, were obtained for the trait under selection, but biased estimates were derived for a correlated trait that was analyzed separately. When an effect of the QTL was simulated only on the trait under selection, a “ghost” effect was also found for the correlated trait. Furthermore, if an effect was simulated only for the correlated trait, then the statistical power was less than that obtained with a random sample of equal size. With multiple-trait analyses, the power of quantitative-trait locus detection was always greater with selective genotyping. Received: 23 February 1998 / Accepted: 15 May 1998     

铁线蕨中间纤维的研究及某些植物类角蛋白的比较分析

应用整装电镜制样技术,结合选择性抽提方法在铁线蕨（ＡｄｉａｎｔｕｍｐｈｉｌｉｐｐｅｎｓｅＬ．）叶细胞中观察到直径１０ｎｍ的纤维网络结构。免疫印迹结果显示：经选择性抽提得到的纤维蛋白与动物角蛋白抗体有免疫交叉反应,间接免疫荧光标记也得到类似结果,而且此类蛋白能在体外自组装为１０ｎｍ或更粗的纤维。说明蕨类植物细胞中存在类角蛋白中间纤维网络。免疫印迹结果表明,螺旋藻（ＳｐｉｒｕｌｉｎａｓｕｂｔｉｌｌｉｓｉｎａＫｕｔｚ．）细胞,地钱（ＭａｒｃｈａｎｔｉａｐｏｌｙｍｏｒｐｈａＬ．）叶状体,铁线蕨（Ａ．ｐｈｉｌｉｐｐｅｎｓｅＬ．）、银杏（ＧｉｎｋｇｏｂｉｌｏｂａＬ．）、白菜（ＢｒａｓｉｃａｐｅｋｉｎｅｎｓｉｓＲｕｐｒ．）的叶组织经选择性抽提后得到的蛋白均与动物角蛋白抗体有免疫交叉反应。其中,螺旋藻仅含有两种类酸性角蛋白,而其余４种植物材料均含有３种类酸性角蛋白及３种类碱性角蛋白。结合以往实验结果,我们认为类角蛋白在植物细胞中是普遍存在的。     

选择性冠状静脉动脉化搭桥术中不同移植物的应用疗效比较

目的:对比选择性冠状静脉动脉化(SCVBG)搭桥治疗弥漫性右冠状动脉狭窄病变中选择乳内动脉和大隐静脉作为桥血管的治疗效果。方法:选择2008年10月到2014年10月在我院行SCVBG搭桥的84例患者资料,其中选择大隐静脉作为桥血管进行冠状静脉动脉化搭桥患者46例(大隐静脉桥组),选择乳内动脉作为桥血管进行冠状静脉动脉化搭桥患者38例(乳内动脉桥组)。随访记录两组患者的生存情况、近期复查超声心动图、冠状动脉CTA及心绞痛复发率。结果:乳内动脉桥组患者总生存率(100%)明显高于大隐静脉桥组(82.6%)(P0.05)。乳内动脉桥组患者桥血管和心中静脉通畅率(100%)明显大于大隐静脉桥组(54.35%)(P0.05)。两组患者左心室射血分数(LVEF)较治疗前明显增加,左心室舒张期末内径(LVEDD)较治疗前明显减小(P0.05)。治疗后,乳内动脉桥组患者心绞痛复发率明显小于大隐静脉桥组(P0.05)。结论:SCVBG搭桥治疗弥漫性右冠状动脉狭窄病变中,选择乳内动脉桥效果优于大隐静脉桥,能明显提高桥血管和心中静脉通畅率,降低心绞痛复发率。     

Selective separation and enrichment of peptides for MS analysis using the microspheres composed of Fe3O4@nSiO2 core and perpendicularly aligned mesoporous SiO2 shell

In this work, we report the development of a novel enrichment protocol for peptides by using the microspheres composed of Fe₃O₄@nSiO₂ Core and perpendicularly aligned mesoporous SiO₂ shell (designated Fe₃O₄@nSiO₂@mSiO₂). The Fe₃O₄@nSiO₂@mSiO₂ microspheres possess useful magnetic responsivity which makes the process of enrichment fast and convenient. The highly ordered nanoscale pores (2 nm) and high‐surface areas of the microspheres were demonstrated to have good size‐exclusion effect for the adsorption of peptides. An increase of S/N ratio over 100 times could be achieved by using the microspheres to enrich a standard peptide, and the application of the microspheres to enrich universal peptides was performed by using myoglobin tryptic digest solution. The enrichment efficiency of re‐used Fe₃O₄@nSiO₂@mSiO₂ microspheres was also studied. Large‐scale enrichment of endogenous peptides in rat brain extract was achieved by the microspheres. Automated nano‐LC‐ESI‐MS/MS was applied to analyze the sample after enrichment, and 60 unique peptides were identified in total. The facile and low‐cost synthesis as well as the convenient and efficient enrichment process of the novel Fe₃O₄@nSiO₂@mSiO₂ microspheres makes it a promising candidate for selectively isolation and enrichment of endogenous peptides from complex biological samples.     

Extracellular hydrophobic regions in scavenger receptor BI play a key role in mediating HDL-cholesterol transport

The binding of high density lipoprotein (HDL) to scavenger receptor BI (SR-BI) is responsible for whole-body cholesterol disposal via reverse cholesterol transport. The extracellular domain of SR-BI is required for HDL binding and selective uptake of HDL-cholesterol. We identified six highly hydrophobic regions in this domain that may be important for receptor activity and performed site-directed mutagenesis to investigate the importance of these regions in SR-BI-mediated cholesterol transport. Non-conservative mutation of the regions encompassing V67, L140/L142, V164 or V221 reduced hydrophobicity and impaired the ability of SR-BI to bind HDL, mediate selective uptake of HDL-cholesterol, promote cholesterol efflux, and enlarge the cholesterol oxidase-sensitive pool of membrane free cholesterol. In contrast, conservative mutations at V67, V164 or V221 did not affect the hydrophobicity or these cholesterol transport activities. We conclude that the hydrophobicity of N-terminal extracellular regions of SR-BI is critical for cholesterol transport, possibly by mediating receptor-ligand and/or receptor-membrane interactions.     

Coalescent Size Versus Coalescent Time with Strong Selection

This work studies the coalescent (ancestral pedigree, genealogy) of the entire population. The coalescent structure (topology) is robust, but selection changes the rate of coalescence (the time between branching events). The change in the rate of coalescence is not uniform, rather the reduction in the time between branching events is greatest when the coalescent is small (immediately after the common ancestor is the only member of the coalescent) with little change when the coalescent is large (immediately preceding when that common ancestor becomes fixed and the size of the coalescent is N). This provides that the reduction in the coalescent time due to selection is much greater than the reduction in the cumulative size of the coalescent (total number of ancestors of the present population after and including the most recent common ancestor) due to selection. If Ns≫1, the coalescent and fixation times are approximately equal to , which is much less than the value N which would result from neutral drift (N rather than the canonical haploid neutral fixation time 2N is the appropriate comparison for the model considered here), in particular, it is 70% less for Ns=10 and 95% less for Ns=100. However, for those values of Ns, and N ranging between 10³ and 10⁶, the reduction in the cumulative size of the coalescent of the entire population compared to the neutral case ranges from 17% to 65% (depending on the values of N and s). The coalescent time for two individuals for Ns of 10 and 100 is reduced by approximately 70% and 94%, respectively, compared with the neutral case. Because heterozygosity is proportional to the coalescent time for two individuals and the number of segregating alleles is proportional to the cumulative size of the coalescent, selection reduces heterozygosity more than it reduces the number of segregating alleles.     

A novel strategy for defining haplotypes by selective depletion using restriction enzymes

Various single nucleotide polymorphisms (SNPs) have been investigated regarding association with gene expression levels or human diseases. Although different SNPs within one gene are frequently analyzed individually, it is highly probable that in the majority of the cases, a precise combination of SNP alleles, i.e., haplotype, determines a functional trait. Methods commonly used for haplotype determination, involving studies in families, cloning, or somatic cell hybrids, are expensive and time-consuming. We herein suggest a novel and simple strategy for haplotype determination, involving selective haplotype depletion with a restriction enzyme, followed by sequencing. We studied 11 LTA gene polymorphisms in 102 Brazilian individuals, and we applied this novel methodology for haplotyping 67 out of 70 LTA heterozygous individuals. We concluded that the method is rapid and efficient, and, as it includes only simple and widespread-used techniques, it could be used in most of the laboratories without further investment in equipments. The wider usage of haplotyping could be important to clarify contradictory results frequently observed among studies that focus on a single SNP. Maria Gerbase-DeLima and Andrey Morgun are co-senior authors.     

Synthesis and characterization of metal ion imprinted nano-porous polymer for the selective recognition of copper

Selective recognition of metal ions utilizing metal ion-imprinted polymers (MIIPs) received much importance in diverse fields owing to their high selectivity for the target metal ions. In the present study, a copper ion imprinted polymer was synthesized without an additional complexing ligand or complex with a broad aim to avoid the conventional extra metal ion complexing ligand during the synthesis of MIIP. The complete removal of the copper metal ion from the MIIP was confirmed by AAS and SEM–EDX. SEM image of the MIIP exhibited nano-patterns and it was also found to be entirely different from that of non-imprinted polymer and polymer with copper metal ions. BET surface area analysis revealed more surface area (47.96 m²/g) for the Cu(II)-MIIP than non-imprinted control polymer (41.43 m²/g). TGA result of polymer with copper metal ion indicated more char yield (18.41%) when compared to non-imprinted control polymer (8.3%) and Cu(II)-MIIP (less than 1%). FTIR study confirmed the complexation between Cu(II)-MIIP and Cu(II) metal ion through carbonyl oxygen of acryl amide. The Cu(II)-MIIP exhibited an imprinting efficiency of 2.0 and it was showing 8% interference from a mixture of Zn, Ni and Co ions. A potentiometric ion selective electrode devised with Cu(II)-MIIP showed more potential response for Cu(II) ion than that was fabricated from non-imprinted polymer.     

Biodesulfurization of refractory organic sulfur compounds in fossil fuels

The stringent new regulations to lower sulfur content in fossil fuels require new economic and efficient methods for desulfurization of recalcitrant organic sulfur. Hydrodesulfurization of such compounds is very costly and requires high operating temperature and pressure. Biodesulfurization is a non-invasive approach that can specifically remove sulfur from refractory hydrocarbons under mild conditions and it can be potentially used in industrial desulfurization. Intensive research has been conducted in microbiology and molecular biology of the competent strains to increase their desulfurization activity; however, even the highest activity obtained is still insufficient to fulfill the industrial requirements. To improve the biodesulfurization efficiency, more work is needed in areas such as increasing specific desulfurization activity, hydrocarbon phase tolerance, sulfur removal at higher temperature, and isolating new strains for desulfurizing a broader range of sulfur compounds. This article comprehensively reviews and discusses key issues, advances and challenges for a competitive biodesulfurization process.